----> ENTRY HEADER:@M70116:5:000000000-AHW3T:1:1101:15009:1805 1:N:0:1
Threads: 1 (effective)  1 (requested)
IDX = 0: reading from 0 to 2028853778
Staggering at 125000 reads; processed 125000 reads
IDX(0) counted 5811040 reads
GLOBAL READ COUNT = 5811040
Trim Time: 192251 ms

PROGRAM ELAPSED TIME: 210575 ms
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 4079050 sequences (140000034 bp)...
[M::process] read 4066592 sequences (140000004 bp)...
[M::mem_process_seqs] Processed 4079050 reads in 186.348 CPU sec, 17.522 real sec
[M::mem_process_seqs] Processed 4066592 reads in 181.257 CPU sec, 16.055 real sec
[M::process] read 3914386 sequences (140000031 bp)...
[M::mem_process_seqs] Processed 3914386 reads in 178.691 CPU sec, 12.785 real sec
[M::process] read 1262453 sequences (45226727 bp)...
[M::mem_process_seqs] Processed 1262453 reads in 56.840 CPU sec, 4.316 real sec
[main] Version: 0.7.12-r1044
[main] CMD: bwa mem -k 30 -T 0 -B 100 -O 100 -E 100 -t 14 /home/src/gottcha/database/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species -
[main] Real time: 138.839 sec; CPU: 648.870 sec

Parsing ./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA_splitrim.stats.txt... found 5811040 reads (split-trimmed: 13322481) and 462364057 bases.
->Retrieving parsed DB from disk [/home/src/gottcha/database/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.parsedGOTTCHA.dmp]...done. 16 wallclock secs (13.96 usr +  2.05 sys = 16.01 CPU)
->Parsing SAM file [-] done. Mapped split-trimmed reads: 93473; Mapped split-trimmed reads to plasmids: 5827; Unmapped split-trimmed reads: 13196857; Mapped raw reads: 39633; Mapped raw reads to plasmids: 2179
. 123 wallclock secs (83.35 usr +  1.75 sys = 85.10 CPU)
->Consolidating hits...done.  0 wallclock secs ( 0.41 usr +  0.00 sys =  0.41 CPU)
->Retrieving Genome Vitals from disk [/home/src/gottcha/database/genomeVitals.dmp]...done.  1 wallclock secs ( 0.24 usr +  0.02 sys =  0.26 CPU)
->Storing coordinates to disk [./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.replicon.contig.coords.csv]...done.  1 wallclock secs ( 1.11 usr +  0.02 sys =  1.13 CPU)
->Storing datastructure GI coordinates to disk in BINARY format as "./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.giCoords.dmp"...done. 0 wallsecs
->Storing datastructure contig length histogram (by entry) to disk in BINARY format as "./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.replicon.contig.HistoByEntry.dmp"...done. 0 wallsecs
->Storing datastructure contig length histogram (by GI) to disk in BINARY format as "./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.replicon.contig.HistoByGI.dmp"...done. 0 wallsecs
->Storing parseable contig length histogram(s) to disk...done.  1 wallclock secs ( 0.12 usr +  0.00 sys =  0.12 CPU)
->Calculating non-overlapping coverage from mapping results...done.  0 wallclock secs ( 0.01 usr +  0.00 sys =  0.01 CPU)
===== REPLICON-level Analysis =====
->Writing REPLICON-level results to disk [./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.replicon.tsv]...Use of uninitialized value in concatenation (.) or string at /net/clusterhn.cluster.com/home/s
rc/gottcha/bin/profileGottcha.pl line 1355.
Use of uninitialized value in concatenation (.) or string at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1355.
Use of uninitialized value in concatenation (.) or string at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1355.
Use of uninitialized value in concatenation (.) or string at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1355.
Use of uninitialized value in concatenation (.) or string at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1355.
Use of uninitialized value in concatenation (.) or string at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1355.
Use of uninitialized value in concatenation (.) or string at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1355.
Use of uninitialized value in concatenation (.) or string at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1355.
done.  0 wallclock secs ( 0.19 usr +  0.00 sys =  0.19 CPU)
===== Extended Taxonomic Rank-level Analysis =====
->Pulling replicon GIs from DB entries...done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Mapping replicon GIs to source organisms...done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Retrieving Tax Tree from disk [/home/src/gottcha/database/speciesTreeGI.dmp]...done.  6 wallclock secs ( 5.60 usr +  0.15 sys =  5.75 CPU)
->Mapping source organism to its tax tree...done.  3 wallclock secs ( 3.66 usr +  0.01 sys =  3.67 CPU)
  Congratulations! All organisms have been identified!
->Rolling up results for rank STRAIN [./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.strain.tsv]...Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha
/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
done. 12 wallclock secs (11.54 usr +  0.01 sys = 11.55 CPU)
->Rolling up results for rank SPECIES [./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.species.tsv]...Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottc
ha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
done. 13 wallclock secs (11.68 usr +  0.01 sys = 11.69 CPU)
->Rolling up results for rank GENUS [./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.genus.tsv]...Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/b
in/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
done. 12 wallclock secs (11.67 usr +  0.01 sys = 11.68 CPU)
->Rolling up results for rank FAMILY [./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.family.tsv]...Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha
/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
done. 12 wallclock secs (11.63 usr +  0.01 sys = 11.64 CPU)
->Rolling up results for rank ORDER [./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.order.tsv]...Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/b
in/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
done. 12 wallclock secs (11.63 usr +  0.01 sys = 11.64 CPU)
->Rolling up results for rank CLASS [./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.class.tsv]...Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/b
in/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
done. 12 wallclock secs (11.60 usr +  0.01 sys = 11.61 CPU)
->Rolling up results for rank PHYLUM [./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.phylum.tsv]...Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha
/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1630.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1641.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1652.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1663.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1674.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1685.
Use of uninitialized value $readcount in addition (+) at /net/clusterhn.cluster.com/home/src/gottcha/bin/profileGottcha.pl line 1696.
done. 12 wallclock secs (11.59 usr +  0.01 sys = 11.60 CPU)
Saving updated table to "./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.strain.tsv.ABU"...done. (982 taxonomie(s), 857 filtered)
Saving updated table to "./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.species.tsv.ABU"...done. (694 taxonomie(s), 644 filtered)
Saving updated table to "./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.genus.tsv.ABU"...done. (378 taxonomie(s), 354 filtered)
Saving updated table to "./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.family.tsv.ABU"...done. (190 taxonomie(s), 181 filtered)
Saving updated table to "./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.order.tsv.ABU"...done. (103 taxonomie(s), 101 filtered)
Saving updated table to "./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.class.tsv.ABU"...done. (47 taxonomie(s), 47 filtered)
Saving updated table to "./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.phylum.tsv.ABU"...done. (22 taxonomie(s), 22 filtered)
------------------
TOTAL SCRIPT TIME:  -   245 wallclock secs (197.96 usr +  4.10 sys = 202.06 CPU)
------------------
Loading STRAIN Lookup file...done!
Loading SPECIES Lookup file...done!
Loading GENUS Lookup file...done!
Loading FAMILY Lookup file...done!
Loading ORDER Lookup file...done!
Loading CLASS Lookup file...done!
Loading PHYLUM Lookup file...done!
Loading TAX Lookup file...done!
Parsing table "./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.strain.tsv"...Done!


STRAIN  LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
Achromobacter xylosoxidans NH44784-1996 22760   35054   1036    0   478 1.54015817223199    0.00357819272541293
Acidovorax ebreus TPSY  1155    1502    45  0   18  1.3004329004329 0.0030212478355215
Acidovorax sp. JS42 chromosome  2526    3577    106 0   34  1.41607284243864    0.00328990985135359
Acinetobacter baumannii 1656-2  2213    4991    155 30  63  2.25530953456846    0.0052396775315956
Acinetobacter baumannii AB0057  174 323 10  0   2   1.85632183908046    0.00431272412170298
Acinetobacter baumannii AB307-0294  20267   28334   871 0   393 1.3980362165096 0.00324800602299759
Acinetobacter baumannii ACICU   2663    5493    167 117 65  2.06271122793842    0.00479222098321281
Acinetobacter baumannii ATCC 17978  1988    4225    131 42  52  2.12525150905433    0.00493751851366705
Acinetobacter baumannii AYE 10569   21521   653 579 222 2.03623805468824    0.00473071683535954
Acinetobacter baumannii BJAB07104   622 1444    45  0   11  2.32154340836013    0.00539355624980141
Acinetobacter baumannii BJAB0715    4481    21855   670 643 266 4.87725954028119    0.0113311573587887
Acinetobacter baumannii BJAB0868    2749    6947    213 160 71  2.52710076391415    0.00587112007899735
Acinetobacter baumannii MDR-TJ  873 1865    56  53  26  2.13631156930126    0.00496321394406616
Acinetobacter baumannii MDR-ZJ06    1613    5037    153 1   77  3.12275263484191    0.00725497612044767
Acinetobacter baumannii ZW85-1  1404    2279    69  42  34  1.62321937321937    0.00377116575279129
Acinetobacter calcoaceticus PHEA-2  11902   16629   513 0   282 1.39716014115275    0.00324597066940514
Aeromonas hydrophila subsp. hydrophila ATCC 7966    7833    12659   385 0   247 1.61611132388612    0.00375465188371299
Aeromonas salmonicida subsp. salmonicida A449   4088    6325    188 25  102 1.54721135029354    0.00359457911408776
Akkermansia muciniphila ATCC BAA-835    4712    8073    233 0   85  1.71328522920204    0.00398041243699271
Alistipes shahii WAL 8301   4313    5701    165 0   52  1.32181776025968    0.00307093049230686
Alteromonas macleodii str. 'Deep ecotype'   493 911 26  0   5   1.84787018255578    0.00429308869954989
Arthrobacter arilaitensis Re117 5577    9124    276 3   134 1.63600502062041    0.00380087017623617
Bacillus cereus AH820   376 440 13  0   3   1.17021276595745    0.00271871219581697
Bacillus infantis NRRL B-14911  13265   21660   652 0   184 1.6328684508104 0.00379358309918185
Bacillus megaterium WSH-002 6468    10825   334 18  130 1.67362399505257    0.00388826895324333
Bacillus thuringiensis BMB171   196 393 12  0   2   2.00510204081633    0.00465837968171942
Bacteroides fragilis NCTC 9343  7061    23141   687 7   200 3.27729783316811    0.00761402528459741
Bacteroides fragilis YCH46  2347    3500    107 0   36  1.49126544524925    0.00346460205455237
Bacteroides thetaiotaomicron VPI-5482   12341   20991   624 5   201 1.70091564703022    0.00395167464256252
Bacteroides vulgatus ATCC 8482  40516   74677   2220    0   593 1.84314838582288    0.00428211872320257
Bifidobacterium adolescentis ATCC 15703 5447    9431    283 0   84  1.73141178630439    0.00402252519912961
Bifidobacterium bifidum BGN4    507 572 18  0   3   1.12820512820513    0.00262111739904406
Bifidobacterium longum DJO10A   500 639 19  0   6   1.278   0.00296913030461713
Bifidobacterium longum NCC2705  4978    9859    288 0   93  1.98051426275613    0.00460125580303261
Bifidobacterium longum subsp. infantis 157F 256 2130    60  60  13  8.3203125   0.0193302754206845
Bifidobacterium longum subsp. longum BBMN68 737 1256    37  0   13  1.70420624151967    0.00395931955947866
Buchnera aphidicola str. Sg (Schizaphis graminum)   562 807 24  0   9   1.43594306049822    0.00333607359673704
Capnocytophaga canimorsus Cc5   6692    12161   368 0   126 1.81724447101016    0.00422193711249938
Carnobacterium sp. WN1359   11661   16454   492 0   144 1.4110282137038 0.00327818985131278
Carnobacterium sp. WN1359 plasmid pWNCR12   365 1762    53  53  19  4.82739726027397    0.0112153141611152
Carnobacterium sp. WN1359 plasmid pWNCR15   378 548 16  16  6   1.44973544973545    0.00336811694639067
Carnobacterium sp. WN1359 plasmid pWNCR64   756 841 27  27  8   1.11243386243386    0.00258447659846218
Chroococcidiopsis thermalis PCC 7203    26595   43232   1291    6   436 1.62556871592405    0.00377662389412179
Comamonas testosteroni CNB-2    62936   144679  4288    0   1689    2.29882738019575    0.00534078093867201
Corynebacterium aurimucosum ATCC 700975 4382    6867    212 35  139 1.56709265175719    0.00364076860913544
Corynebacterium callunae DSM 20147  3106    7186    217 0   71  2.31358660656793    0.00537507050541249
Corynebacterium diphtheriae CDCE 8392   410 707 21  0   4   1.72439024390244    0.00400621230841695
Corynebacterium diphtheriae HC02    529 702 22  0   6   1.32703213610586    0.00308304485955612
Corynebacterium glutamicum MB001    3413    7507    226 0   66  2.19953120421916    0.00511008979217381
Corynebacterium jeikeium K411   2838    4042    123 0   57  1.42424242424242    0.00330888993970231
Cronobacter sakazakii CMCC 45402    1207    1596    48  1   16  1.32228666114333    0.00307201987245045
Cronobacter sakazakii SP291 455 587 17  14  8   1.29010989010989    0.00299726476604973
Delftia acidovorans SPH-1   10812   24332   706 0   275 2.2504624491306 0.00522841647661702
Delftia sp. Cs1-4 chromosome    6831    10304   304 0   137 1.50841750841751    0.00350445081084311
Edwardsiella tarda FL6-60   406 820 26  0   16  2.01970443349754    0.00469230488252513
Enterobacter cloacae EcWSU1 3456    5801    176 2   87  1.67853009259259    0.00389966710886422
Enterobacter cloacae subsp. cloacae ATCC 13047  2022    2588    76  37  33  1.27992087042532    0.00297359299209058
Enterobacter cloacae subsp. cloacae ENHKU01 6330    8376    260 0   171 1.32322274881517    0.0030741946504428
Enterococcus casseliflavus EC20 28059   51675   1562    0   535 1.84165508393029    0.00427864938994494
Enterococcus hirae ATCC 9790    19024   28741   866 0   253 1.51077586206897    0.00350992988697421
Erwinia billingiae Eb661    6033    12721   391 7   170 2.10856953422841    0.00489876189629891
Erwinia sp. Ejp617 chromosome   695 1280    40  0   15  1.84172661870504    0.00427881558405099
Escherichia coli 536    647 767 25  0   9   1.1854714064915 0.00275416203307591
Escherichia coli APEC O1    171 544 17  1   6   3.1812865497076 0.00739096580783077
Escherichia coli APEC O78   334 502 15  0   2   1.50299401197605    0.0034918506014211
Escherichia coli BL21(DE3) uid161949    1033    1474    43  0   18  1.4269119070668 0.00331509185077547
Escherichia coli ETEC H10407    937 1281    40  20  17  1.36712913553895    0.00317620074073062
Escherichia coli HS 463 763 23  0   11  1.64794816414687    0.00382861724147624
Escherichia coli IAI39  265 572 19  0   3   2.15849056603774    0.0050147415898692
Escherichia coli NA114  383 409 12  0   3   1.06788511749347    0.00248097814100117
Escherichia coli O139:H28 str. E24377A  684 1153    36  17  17  1.68567251461988    0.00391626083475592
Escherichia coli O55:H7 str. CB9615 188 302 10  10  3   1.6063829787234 0.00373205037789421
Escherichia coli O83:H1 str. NRG 857C   991 1490    44  0   13  1.50353178607467    0.00349309999216701
Escherichia coli P12b   777 1082    32  0   10  1.39253539253539    0.00323522616136835
Escherichia coli SE11   298 415 13  13  6   1.39261744966443    0.00323541680167237
Escherichia coli SE15   2068    2881    87  0   47  1.3931334622824 0.00323661563477219
Escherichia coli SMS-3-5    488 537 16  8   5   1.10040983606557    0.0025565416210963
Escherichia coli UMNK88 416 470 12  5   7   1.12980769230769    0.0026248405771677
Escherichia coli str. 'clone D i14' 755 4657    133 0   39  6.1682119205298 0.0143303794511312
Escherichia coli str. K-12 substr. MDS42    408 860 27  0   15  2.1078431372549 0.0048970742849787
Eubacterium rectale ATCC 33656  16623   24962   750 0   254 1.50165433435601    0.00348873817777473
Exiguobacterium sp. AT1b chromosome 6667    11293   348 0   133 1.69386530673466    0.00393529484676486
Exiguobacterium sp. MH3 7689    11734   357 0   154 1.52607621277149    0.0035454766279305
Flavobacteriaceae bacterium 3519-10 6737    9694    292 0   132 1.43891940032655    0.00334298841737957
Gardnerella vaginalis 409-05    10810   20057   601 0   155 1.85541165587419    0.00431060952660087
Gardnerella vaginalis ATCC 14019    8976    14205   423 0   128 1.58255347593583    0.0036766881722052
Gardnerella vaginalis HMP9231   875 1527    46  0   16  1.74514285714286    0.00405442609000703
Gordonia sp. KTR9 plasmid pGKT3 998 2112    64  64  18  2.11623246492986    0.0049165649008121
Haemophilus parainfluenzae T3T1 2402    3466    109 0   52  1.44296419650291    0.00335238554328194
Klebsiella oxytoca E718 2010    2778    83  31  31  1.38208955223881    0.00321095772554536
Klebsiella oxytoca KCTC 1686    23627   34960   1056    0   524 1.47966309730393    0.00343764674712735
Klebsiella pneumoniae 342   1122    1283    36  31  18  1.14349376114082    0.00265663691654447
Klebsiella pneumoniae CG43  16439   24867   746 0   406 1.51268325323925    0.00351436125859115
Klebsiella pneumoniae JM45  2204    3243    89  10  26  1.47141560798548    0.00341848565912076
Klebsiella pneumoniae KCTC 2242 484 575 18  7   11  1.18801652892562    0.00276007502223718
Klebsiella pneumoniae subsp. pneumoniae HS11286 1953    3224    98  81  33  1.65079365079365    0.00383522805574412
Klebsiella pneumoniae subsp. pneumoniae MGH 78578   5141    7941    227 212 78  1.54464112040459    0.0035886077937019
Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044  571 662 20  0   8   1.15936952714536    0.00269352049866739
Klebsiella pneumoniae subsp. rhinoscleromatis SB3432    628 746 23  12  15  1.18789808917197    0.00275979985552214
Lactobacillus acidophilus La-14 2464    3320    101 0   39  1.3474025974026 0.00313037080161807
Lactobacillus amylovorus GRL 1112   581 877 26  0   6   1.50946643717728    0.00350688774837678
Lactobacillus crispatus ST1 14036   21433   636 0   198 1.52700199487033    0.00354762746336489
Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365    2832    4837    139 0   43  1.7079802259887 0.00396808751852103
Lactobacillus helveticus DPC 4571   2195    2717    83  0   29  1.2378132118451 0.00287576582061405
Lactobacillus johnsonii NCC 533 331 361 11  0   3   1.09063444108761    0.00253383080617559
Lactobacillus plantarum 16  7710    11827   349 9   95  1.53398184176394    0.00356384348443954
Lactobacillus plantarum JDM1    434 626 19  0   4   1.44239631336406    0.0033510662013124
Lactobacillus reuteri DSM 20016 990 1852    59  0   19  1.87070707070707    0.00434614480023311
Lactobacillus reuteri I5007 3895    5862    183 1   81  1.50500641848524    0.00349652595130502
Lactobacillus reuteri SD2112    221 716 21  21  4   3.23981900452489    0.00752695210313721
Lactobacillus salivarius UCC118 427 1043    34  34  9   2.44262295081967    0.00567485588891394
Lactococcus lactis subsp. cremoris A76  1011    1943    59  38  14  1.92185954500495    0.00446498545875734
Lactococcus lactis subsp. cremoris MG1363   241 338 11  0   3   1.40248962655602    0.00325835246644651
Lactococcus lactis subsp. cremoris SK11 1445    2887    86  86  20  1.99792387543253    0.00464170291460471
Lactococcus lactis subsp. cremoris UC509.9  20488   32519   975 83  259 1.58722178836392    0.00368753389043812
Lactococcus lactis subsp. lactis CV56   1195    1660    48  28  13  1.38912133891213    0.0032272944163962
Lactococcus lactis subsp. lactis Il1403 8117    12805   384 0   112 1.57755328323272    0.00366507140875941
Lactococcus lactis subsp. lactis KF147  599 1163    36  23  11  1.94156928213689    0.00451077636471548
Lactococcus lactis subsp. lactis KLDS 4.0325    301 425 13  0   4   1.41196013289037    0.00328035494481692
Leuconostoc citreum KM20    6455    12293   369 5   97  1.90441518202943    0.00442445761309589
Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293    5530    8410    247 0   66  1.52079566003617    0.00353320851435336
Methylobacterium extorquens AM1 6074    8280    251 141 103 1.36318735594337    0.00316704294945411
Methylobacterium extorquens CM4 1685    2384    69  19  33  1.41483679525223    0.00328703818847478
Methylobacterium extorquens DM4 2842    6911    209 149 70  2.43173821252639    0.00564956777754899
Methylobacterium extorquens PA1 15236   29618   903 0   601 1.94394854292465    0.0045163040136259
Methylobacterium populi BJ001   6583    10103   294 39  118 1.53471061825915    0.00356553662401483
Methylobacterium radiotolerans JCM 2831 8426    12052   364 23  219 1.43033467837645    0.00332304384922718
Micrococcus luteus NCTC 2665    5068    7254    218 0   101 1.43133385951066    0.00332536520993559
Morganella morganii subsp. morganii KT  12321   18477   531 0   158 1.49963476990504    0.00348404619810845
Mycobacterium abscessus subsp. bolletii 50594   161 407 11  11  4   2.52795031055901    0.00587309379941083
Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111 5667    8432    249 0   145 1.48791247573672    0.00345681222404367
Ochrobactrum anthropi ATCC 49188    11415   19274   563 102 229 1.68848007008322    0.0039227835249031
Oscillatoria nigro-viridis PCC 7112 19402   26313   810 63  477 1.35620039171219    0.00315081039293138
Pantoea ananatis AJ13355    4641    7010    209 1   85  1.51045033397975    0.00350917359956051
Pantoea ananatis PA13   682 1072    30  11  15  1.57184750733138    0.0036518153898705
Pantoea vagans C9-1 14513   22007   685 50  474 1.51636463859988    0.00352291408553732
Parabacteroides distasonis ATCC 8503    6058    12934   378 0   116 2.13502806206669    0.00496023201900641
Peptoclostridium difficile 630  407 667 20  0   11  1.63882063882064    0.00380741159824286
Plautia stali symbiont DNA  4760    6295    195 0   108 1.32247899159664    0.00307246670670508
Porphyromonas gingivalis TDC60  9126    14693   460 0   236 1.61001534078457    0.0037404893108153
Porphyromonas gingivalis W83    341 702 22  0   9   2.05865102639296    0.00478278806658412
Prevotella melaninogenica ATCC 25845    6946    12657   388 0   145 1.8221998272387 0.00423344970901606
Propionibacterium acnes ATCC 11828  101136  243275  7208    0   3174    2.40542437905395    0.00558843381792952
Propionibacterium acnes HL096PA1    910 1238    36  11  15  1.36043956043956    0.00316065909741871
Propionibacterium acnes KPA171202   1507    3283    93  0   31  2.178500331785  0.005061229541253
Propionibacterium acnes TypeIA2 P.acn33 11108   17379   507 0   193 1.56454807346057    0.00363485688414877
Pseudomonas aeruginosa B136-33  362 414 12  0   7   1.14364640883978    0.00265699155731827
Pseudomonas aeruginosa LES431   836 1532    42  0   12  1.83253588516746    0.00425746309150947
Pseudomonas aeruginosa M18  677 1141    34  0   11  1.68537666174298    0.00391557349066945
Pseudomonas aeruginosa PA1R 1816    2243    67  0   27  1.23513215859031    0.00286953702838628
Pseudomonas aeruginosa PA7  3932    11997   355 0   93  3.05111902339776    0.00708855239073876
Pseudomonas aeruginosa PAO581   38850   70705   2081    0   829 1.81994851994852    0.00422821932975137
Pseudomonas aeruginosa RP73 1043    2373    70  0   16  2.2751677852349 0.00528581347357558
Pseudomonas aeruginosa SCV20265 911 1259    35  0   11  1.38199780461032    0.00321074457166107
Pseudomonas aeruginosa c7447m   1301    1775    54  0   19  1.36433512682552    0.00316970952324829
Pseudomonas fluorescens A506    17112   27518   826 0   384 1.60811126694717    0.0037360656462356
Pseudomonas mendocina NK-01 3438    4246    129 0   83  1.23502036067481    0.00286927729240905
Pseudomonas mendocina ymp   4256    5513    172 0   123 1.2953477443609 0.00300943367981174
Pseudomonas monteilii SB3101    1205    1700    52  0   20  1.41078838174274    0.00327763265855566
Pseudomonas putida BIRD-1   11567   17685   553 0   353 1.5289184749719 0.00355207995096095
Pseudomonas putida F1   3637    4642    139 0   74  1.2763266428375 0.00296524265558614
Pseudomonas putida GB-1 3848    5135    156 0   81  1.33445945945946    0.00310030048620038
Pseudomonas putida H8234    34598   56737   1689    0   658 1.63989247933407    0.00380990176580947
Pseudomonas putida HB3267   7175    18328   565 79  309 2.55442508710801    0.00593460167214919
Pseudomonas putida KT2440   3431    5137    153 0   61  1.49723112795103    0.00347846190533295
Pseudomonas putida NBRC 14164   11932   18060   545 0   272 1.5135769359705 0.0035164375187477
Pseudomonas putida ND6  3239    4596    132 6   53  1.41895646804569    0.00329660927246241
Pseudomonas putida S16  3382    6164    185 0   66  1.82259018332348    0.00423435660892287
Pseudomonas putida W619 10860   26623   812 0   413 2.45147329650092    0.00569541757089245
Pseudomonas sp. TKP 7671    13217   395 0   159 1.72298266197367    0.00400294212519242
Pseudomonas sp. VLB120 plasmid pSTY 2199    2992    88  88  35  1.3606184629377 0.00316107473499993
Pseudomonas stutzeri A1501  6801    11556   345 0   155 1.69916188795765    0.00394760019873672
Pseudomonas stutzeri ATCC 17588 = LMG 11199 38553   58075   1719    0   745 1.50636785723549    0.00349968893178332
Pseudomonas stutzeri CCUG 29243 12255   16616   499 0   242 1.35585475316197    0.00315000738362473
Pseudomonas stutzeri DSM 10701  38244   67159   1984    0   881 1.75606631105533    0.00407980414794335
Pseudomonas stutzeri DSM 4166   3795    6113    181 0   68  1.61080368906456    0.00374232085132289
Pseudomonas stutzeri RCH2   10183   18241   543 2   190 1.79131886477462    0.00416170510691291
Psychrobacter cryohalolentis K5 1610    2416    76  55  32  1.50062111801242    0.00348633774431857
Psychrobacter sp. G 1193    1416    46  0   28  1.18692372170997    0.00275753614350394
Psychrobacter sp. G plasmid PsyG_26 550 1195    38  38  12  2.17272727272727    0.00504781720588629
Psychrobacter sp. PRwf-1 chromosome 5428    8267    248 0   92  1.52302873986735    0.00353839654643428
Raoultella ornithinolytica B6   53687   91392   2712    0   1080    1.70231154655689    0.00395491768449275
Rhizobium sp. IRBG74 circular chromosome    6285    12565   371 0   167 1.99920445505171    0.00464467803804352
Rhizobium sp. IRBG74 linear chromosome  5813    10684   316 0   153 1.83794942370549    0.00427004016610138
Rickettsia felis URRWXCal2  406 600 18  0   6   1.47783251231527    0.0034333938164818
Roseburia hominis A2-183    5403    8422    255 0   85  1.55876364982417    0.00362141814587524
Rothia dentocariosa ATCC 17931  10307   20901   625 0   234 2.02784515377899    0.00471121791796258
Rothia mucilaginosa DY-18   10060   14610   445 0   209 1.45228628230616    0.00337404320170186
Salmonella bongori N268-08  750 1226    39  39  14  1.63466666666667    0.00379776082781493
Salmonella enterica subsp. enterica serovar Cubana str. CFSAN002050 3524    40300   1229    57  358 11.4358683314415    0.0265685314730004
Salmonella enterica subsp. enterica serovar Heidelberg str. 41578   269 499 16  16  4   1.85501858736059    0.00430969632500814
Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7   388 948 29  0   10  2.44329896907217    0.00567642645720811
Salmonella enterica subsp. enterica serovar Typhimurium str. U288   335 521 17  17  7   1.55522388059701    0.00361319433047328
Salmonella enterica subsp. enterica serovar Typhimurium var. 5- str. CFSAN001921    288 318 10  10  2   1.10416666666667    0.00256526972718943
Serratia marcescens WW4 4461    6770    208 0   122 1.5175969513562 0.00352577707235232
Shewanella baltica BA175    41818   61667   1879    0   895 1.47465206370462    0.00342600479742692
Shewanella baltica OS155    3607    5736    177 70  79  1.59024119767119    0.00369454877281392
Shewanella baltica OS185    1728    3950    121 0   76  2.28587962962963    0.00531069990691731
Shewanella baltica OS223    2368    4274    132 7   48  1.80489864864865    0.00419325451836089
Shewanella baltica OS678    410 503 15  0   6   1.22682926829268    0.00285024722932635
Shewanella putrefaciens 200 2195    3787    117 0   29  1.725284738041  0.00400829045368621
Shewanella putrefaciens CN-32   2687    5919    181 0   51  2.20282843319687    0.00511775012275205
Shewanella sp. ANA-3 chromosome 1   1738    2646    81  0   30  1.52243958573072    0.00353702778633948
Shewanella sp. ANA-3 plasmid 1  4726    9576    290 290 66  2.0262378332628 0.00470748368943845
Shewanella sp. W3-18-1 chromosome   544 613 18  0   11  1.12683823529412    0.00261794174711507
Solibacillus silvestris StLB046 4462    6374    196 0   113 1.42850739578664    0.00331879859092318
Sphingobacterium sp. 21 chromosome  41998   68651   2058    0   544 1.63462545835516    0.00379766509006336
Sphingobium sp. SYK-6 plasmid pSLPG 483 681 19  19  7   1.40993788819876    0.00327565673824634
Sphingomonas sp. MM-1 plasmid pISP0 766 1432    44  44  20  1.86945169712794    0.00434322823705829
Sphingomonas sp. MM-1 plasmid pISP3 274 673 20  20  10  2.45620437956204    0.00570640912182394
Sphingopyxis alaskensis RB2256  3461    5210    157 1   103 1.50534527593181    0.00349731320632346
Staphylococcus aureus subsp. aureus Mu50    126 334 11  11  5   2.65079365079365    0.00615849120489681
Staphylococcus epidermidis ATCC 12228   14769   23662   727 5   296 1.60213961676485    0.00372219193142737
Staphylococcus epidermidis RP62A    709 1291    38  8   8   1.82087447108604    0.00423037055790708
Staphylococcus haemolyticus JCSC1435    7575    11036   340 5   126 1.45689768976898    0.00338475671472595
Staphylococcus pseudintermedius ED99    7571    12814   390 0   104 1.69251089684322    0.00393214819617521
Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305    5167    9164    283 16  80  1.77356299593575    0.00412045355115836
Staphylococcus warneri SG1  512 715 22  0   7   1.396484375 0.00324440068680502
Stenotrophomonas maltophilia D457   2999    4693    141 0   60  1.56485495165055    0.00363556984293883
Stenotrophomonas maltophilia JV3    38646   65473   1991    0   1282    1.69417274750298    0.00393600911257242
Stenotrophomonas maltophilia K279a  16471   27444   814 0   311 1.6662012021128 0.00387102385194259
Stenotrophomonas maltophilia R551-3 7979    12094   370 0   199 1.51572878806868    0.00352143683742983
Streptococcus lutetiensis 033   3604    6346    188 0   69  1.76082130965594    0.00409085126096641
Streptococcus mitis B6  1110    1515    49  0   30  1.36486486486486    0.0031709402441138
Streptococcus oralis Uo5    1936    5456    163 0   51  2.81818181818182    0.00654737796579394
Streptococcus parasanguinis ATCC 15912  3333    4504    138 0   76  1.35133513351335    0.0031395071178469
Streptococcus pyogenes MGAS10750    150 330 10  0   6   2.2 0.00511117892813591
Streptococcus pyogenes MGAS2096 283 481 15  0   3   1.69964664310954    0.00394872641251747
Streptococcus salivarius JIM8777    2097    2922    92  0   43  1.3934191702432 0.00323727940954895
Streptococcus sanguinis SK36    1771    4338    132 0   55  2.44946357989836    0.00569074847036948
Streptococcus thermophilus CNRZ1066 6833    9536    290 0   129 1.3955802722084 0.00324230021810625
Streptococcus thermophilus MN-ZLW-002   214 449 14  0   2   2.0981308411215 0.0048745100652783
Tannerella forsythia 92A2   3865    5769    170 0   67  1.49262613195343    0.00346776328782972
Veillonella parvula DSM 2008    4607    11541   352 0   143 2.50510093336227    0.00582000868338857
Vibrio cholerae O1 str. 2010EL-1786 377 671 19  0   8   1.77984084880637    0.00413503865538847
Xanthomonas campestris pv. campestris   277 455 14  0   2   1.64259927797834    0.00381619037135189
Yersinia pestis biovar Microtus str. 91001  516 1427    39  39  16  2.76550387596899    0.00642499324387768
Zymomonas mobilis subsp. mobilis NCIMB 11163    376 655 20  20  9   1.74202127659574    0.00404717383695481
=================================================================


SPECIES LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
Achromobacter xylosoxidans  22760   35054   1036    0   478 1.54015817223199    0.00684034208502743
Acidovorax ebreus   1155    1502    45  0   18  1.3004329004329 0.0057756443837806
Acidovorax sp. JS42 2526    3577    106 0   34  1.41607284243864    0.00628923888093906
Acinetobacter baumannii 49616   104314  3193    1667    1282    2.10242663656885    0.00933755874045279
Acinetobacter calcoaceticus 11902   16629   513 0   282 1.39716014115275    0.00620524143906596
Aeromonas hydrophila    7833    12659   385 0   247 1.61611132388612    0.0071776746714574
Aeromonas salmonicida   4088    6325    188 25  102 1.54721135029354    0.0068716675369177
Akkermansia muciniphila 4712    8073    233 0   85  1.71328522920204    0.0076092555091162
Alistipes shahii    4313    5701    165 0   52  1.32181776025968    0.00587062148372582
Alteromonas macleodii   493 911     26  0   5   1.84787018255578    0.0082069909476153
Arthrobacter arilaitensis   5577    9124    276 3   134 1.63600502062041    0.00726602903236118
Bacillus cereus 376 440 13  0   3   1.17021276595745    0.00519729452190926
Bacillus infantis   13265   21660   652 0   184 1.6328684508104 0.0072520985083015
Bacillus megaterium 6468    10825   334 18  130 1.67362399505257    0.00743310710177204
Bacillus thuringiensis  196 393 12  0   2   2.00510204081633    0.00890530863767959
Bacteroides fragilis    9408    26641   794 7   236 2.83173894557823    0.0125766713007009
Bacteroides thetaiotaomicron    12341   20991   624 5   201 1.70091564703022    0.00755431818187958
Bacteroides vulgatus    40516   74677   2220    0   593 1.84314838582288    0.00818601991652817
Bifidobacterium adolescentis    5447    9431    283 0   84  1.73141178630439    0.00768976142963744
Bifidobacterium bifidum 507 572 18  0   3   1.12820512820513    0.00501072497496893
Bifidobacterium longum  6471    13884   404 60  125 2.14557255447381    0.00952918375882004
Buchnera aphidicola 562 807 24  0   9   1.43594306049822    0.00637748896543178
Capnocytophaga canimorsus   6692    12161   368 0   126 1.81724447101016    0.00807097222736541
Carnobacterium sp. WN1359   13160   19605   588 96  177 1.48974164133739    0.0066164259157163
Chroococcidiopsis thermalis 26595   43232   1291    6   436 1.62556871592405    0.00721967801756688
Comamonas testosteroni  62936   144679  4288    0   1689    2.29882738019575    0.0102098381571928
Corynebacterium aurimucosum 4382    6867    212 35  139 1.56709265175719    0.00695996684640344
Corynebacterium callunae    3106    7186    217 0   71  2.31358660656793    0.0102753886695468
Corynebacterium diphtheriae 939 1409    43  0   10  1.50053248136315    0.00666435153692317
Corynebacterium glutamicum  3413    7507    226 0   66  2.19953120421916    0.00976883162704484
Corynebacterium jeikeium    2838    4042    123 0   57  1.42424242424242    0.00632552264402069
Cronobacter sakazakii   1662    2183    65  15  24  1.31347773766546    0.00583358073780125
Delftia acidovorans 10812   24332   706 0   275 2.2504624491306 0.00999503380828292
Delftia sp. Cs1-4   6831    10304   304 0   137 1.50841750841751    0.00669937150005029
Edwardsiella tarda  406 820 26  0   16  2.01970443349754    0.00897016260073367
Enterobacter cloacae    11808   16765   512 39  291 1.41980013550135    0.00630579299860035
Enterococcus casseliflavus  28059   51675   1562    0   535 1.84165508393029    0.00817938767838164
Enterococcus hirae  19024   28741   866 0   253 1.51077586206897    0.00670984571368905
Erwinia billingiae  6033    12721   391 7   170 2.10856953422841    0.00936484134177407
Erwinia sp. Ejp617  695 1280    40  0   15  1.84172661870504    0.00817970538752286
Escherichia coli    11306   20159   604 74  231 1.78303555634177    0.00791903933962166
Eubacterium rectale 16623   24962   750 0   254 1.50165433435601    0.00666933405000438
Exiguobacterium sp. AT1b    6667    11293   348 0   133 1.69386530673466    0.00752300533342869
Exiguobacterium sp. MH3 7689    11734   357 0   154 1.52607621277149    0.0067777995347401
Flavobacteriaceae bacterium 3519-10 6737    9694    292 0   132 1.43891940032655    0.00639070785616272
Gardnerella vaginalis   20661   35789   1070    0   299 1.73220076472581    0.00769326553875919
Gordonia sp. KTR9   998 2112    64  64  18  2.11623246492986    0.00939887490294773
Haemophilus parainfluenzae  2402    3466    109 0   52  1.44296419650291    0.00640867210815277
Klebsiella oxytoca  25637   37738   1139    31  555 1.47201310605765    0.0065376877392314
Klebsiella pneumoniae   28542   42541   1257    353 595 1.49047018428982    0.00661966161131441
Lactobacillus acidophilus   2464    3320    101 0   39  1.3474025974026 0.00598425204544511
Lactobacillus amylovorus    581 877 26  0   6   1.50946643717728    0.00670403013295503
Lactobacillus crispatus 14036   21433   636 0   198 1.52700199487033    0.00678191123337368
Lactobacillus delbrueckii   2832    4837    139 0   43  1.7079802259887 0.00758569426885163
Lactobacillus helveticus    2195    2717    83  0   29  1.2378132118451 0.00549753003233208
Lactobacillus johnsonii 331 361 11  0   3   1.09063444108761    0.00484386136518728
Lactobacillus plantarum 8144    12453   368 9   99  1.52910117878193    0.00679123439012054
Lactobacillus reuteri   5106    8430    263 22  104 1.65099882491187    0.00733262138135409
Lactobacillus salivarius    427 1043    34  34  9   2.44262295081967    0.0108484809350017
Lactococcus lactis  33397   53740   1612    258 436 1.60912656825463    0.00714665310577596
Leuconostoc citreum 6455    12293   369 5   97  1.90441518202943    0.00845812563402024
Leuconostoc mesenteroides   5530    8410    247 0   66  1.52079566003617    0.00675434688698035
Methylobacterium extorquens 25837   47193   1432    309 807 1.82656655184425    0.00811237461252242
Methylobacterium populi 6583    10103   294 39  118 1.53471061825915    0.0068161477305951
Methylobacterium radiotolerans  8426    12052   364 23  219 1.43033467837645    0.00635258032101584
Micrococcus luteus  5068    7254    218 0   101 1.43133385951066    0.00635701800857681
Morganella morganii 12321   18477   531 0   158 1.49963476990504    0.00666036450911145
Mycobacterium abscessus 161 407 11  11  4   2.52795031055901    0.0112274474206214
Nocardiopsis dassonvillei   5667    8432    249 0   145 1.48791247573672    0.00660830199788481
Ochrobactrum anthropi   11415   19274   563 102 229 1.68848007008322    0.00749908775043701
Oscillatoria nigro-viridis  19402   26313   810 63  477 1.35620039171219    0.00602332590406324
Pantoea ananatis    5323    8082    239 12  100 1.51831673868119    0.00674333719305696
Pantoea vagans  14513   22007   685 50  474 1.51636463859988    0.00673466728331575
Parabacteroides distasonis  6058    12934   378 0   116 2.13502806206669    0.00948235224730513
Peptoclostridium difficile  407 667 20  0   11  1.63882063882064    0.00727853410620208
Plautia stali symbiont  4760    6295    195 0   108 1.32247899159664    0.00587355822660307
Porphyromonas gingivalis    9467    15395   482 0   245 1.62617513467836    0.00722237131998286
Prevotella melaninogenica   6946    12657   388 0   145 1.8221998272387 0.00809298057194163
Propionibacterium acnes 114661  265175  7844    11  3413    2.31268696418137    0.0102713930658554
Pseudomonas aeruginosa  49728   93439   2750    0   1025    1.87900176962677    0.00834525642518425
Pseudomonas fluorescens 17112   27518   826 0   384 1.60811126694717    0.00714214382329599
Pseudomonas mendocina   7694    9759    301 0   206 1.26839095399012    0.00563333570491218
Pseudomonas monteilii   1205    1700    52  0   20  1.41078838174274    0.00626576887665862
Pseudomonas putida  93669   163107  4929    85  2340    1.74131249399481    0.00773373368437555
Pseudomonas sp. TKP 7671    13217   395 0   159 1.72298266197367    0.0076523249539956
Pseudomonas sp. VLB120  2199    2992    88  88  35  1.3606184629377 0.00604294799164056
Pseudomonas stutzeri    109831  177760  5271    2   2281    1.6184865839335 0.00718822397188503
Psychrobacter cryohalolentis    1610    2416    76  55  32  1.50062111801242    0.00666474520103716
Psychrobacter sp. G 1743    2611    84  38  40  1.49799196787149    0.00665306829233963
Psychrobacter sp. PRwf-1    5428    8267    248 0   92  1.52302873986735    0.00676426471894326
Raoultella ornithinolytica  53687   91392   2712    0   1080    1.70231154655689    0.00756051782452077
Rhizobium sp. IRBG74    12098   23249   687 0   320 1.92172259877666    0.00853499348648735
Rickettsia felis    406 600 18  0   6   1.47783251231527    0.00656353361029293
Roseburia hominis   5403    8422    255 0   85  1.55876364982417    0.00692297504681046
Rothia dentocariosa 10307   20901   625 0   234 2.02784515377899    0.00900631818043165
Rothia mucilaginosa 10060   14610   445 0   209 1.45228628230616    0.00645007451537942
Salmonella bongori  750 1226    39  39  14  1.63466666666667    0.00726008496827771
Salmonella enterica 4804    42586   1301    100 381 8.8646960865945 0.0393709911133575
Serratia marcescens 4461    6770    208 0   122 1.5175969513562 0.00674014038404071
Shewanella baltica  49931   76130   2324    77  1104    1.52470409164647    0.00677170549969458
Shewanella putrefaciens 4882    9706    298 0   80  1.98811962310528    0.00882988421136498
Shewanella sp. ANA-3    6464    12222   371 290 96  1.8907797029703 0.00839756604803787
Shewanella sp. W3-18-1  544 613 18  0   11  1.12683823529412    0.00500465416011791
Solibacillus silvestris 4462    6374    196 0   113 1.42850739578664    0.00634446476624642
Sphingobacterium sp. 21 41998   68651   2058    0   544 1.63462545835516    0.00725990194879793
Sphingobium sp. SYK-6   483 681 19  19  7   1.40993788819876    0.0062619915589215
Sphingomonas sp. MM-1   1040    2105    64  64  30  2.02403846153846    0.00898941142526386
Sphingopyxis alaskensis 3461    5210    157 1   103 1.50534527593181    0.0066857267189195
Staphylococcus aureus   126 334 11  11  5   2.65079365079365    0.0117730345461662
Staphylococcus epidermidis  15478   24953   765 13  304 1.61215919369428    0.00716012197916631
Staphylococcus haemolyticus 7575    11036   340 5   126 1.45689768976898    0.00647055527190677
Staphylococcus pseudintermedius 7571    12814   390 0   104 1.69251089684322    0.00751698995971717
Staphylococcus saprophyticus    5167    9164    283 16  80  1.77356299593575    0.00787696862586869
Staphylococcus warneri  512 715 22  0   7   1.396484375 0.00620224014235656
Stenotrophomonas maltophilia    66095   109704  3316    0   1852    1.65979272259626    0.00737167793379559
Streptococcus lutetiensis   3604    6346    188 0   69  1.76082130965594    0.00782037866357431
Streptococcus mitis 1110    1515    49  0   30  1.36486486486486    0.00606180764017279
Streptococcus oralis    1936    5456    163 0   51  2.81818181818182    0.0125164596998707
Streptococcus parasanguinis 3333    4504    138 0   76  1.35133513351335    0.00600171771406556
Streptococcus pyogenes  433 811 25  0   9   1.8729792147806 0.00831850830533762
Streptococcus salivarius    2097    2922    92  0   43  1.3934191702432 0.00618862657364969
Streptococcus sanguinis 1771    4338    132 0   55  2.44946357989836    0.0108788623879061
Streptococcus thermophilus  7047    9985    304 0   131 1.41691499929048    0.00629297917272187
Tannerella forsythia    3865    5769    170 0   67  1.49262613195343    0.00662923687429869
Veillonella parvula 4607    11541   352 0   143 2.50510093336227    0.0111259659239327
Vibrio cholerae 377 671 19  0   8   1.77984084880637    0.00790485060706305
Xanthomonas campestris  277 455 14  0   2   1.64259927797834    0.00729531626852836
Yersinia pestis 516 1427    39  39  16  2.76550387596899    0.0122824998692718
Zymomonas mobilis   376 655 20  20  9   1.74202127659574    0.0077368816178422
=================================================================


GENUS   LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
Achromobacter   22760   35054   1036    0   478 1.54015817223199    0.0119318389973243
Acidovorax  3681    5079    151 0   52  1.37978810105949    0.0106894277283268
Acinetobacter   61518   120943  3706    1667    1564    1.96597743749797    0.0152307254407534
Aeromonas   11921   18984   573 25  349 1.59248385202584    0.0123372139763247
Akkermansia 4712    8073    233 0   85  1.71328522920204    0.0132730805704893
Alistipes   4313    5701    165 0   52  1.32181776025968    0.0102403227042364
Alteromonas 493 911 26  0   5   1.84787018255578    0.0143157306202255
Arthrobacter    5577    9124    276 3   134 1.63600502062041    0.0126743790714482
Bacillus    20305   33318   1011    18  319 1.64087663137158    0.0127121201789452
Bacteroides 62265   122309  3638    12  1030    1.96432988035012    0.0152179615655999
Bifidobacterium 12425   23887   705 60  212 1.92249496981891    0.0148938601674933
Buchnera    562 807 24  0   9   1.43594306049822    0.0111244687176255
Capnocytophaga  6692    12161   368 0   126 1.81724447101016    0.0140784685870596
Carnobacterium  13160   19605   588 96  177 1.48974164133739    0.0115412544844582
Chroococcidiopsis   26595   43232   1291    6   436 1.62556871592405    0.0125935274358116
Comamonas   62936   144679  4288    0   1689    2.29882738019575    0.0178093644390994
Corynebacterium 14678   27011   821 35  343 1.84023708952173    0.014256595890575
Cronobacter 1662    2183    65  15  24  1.31347773766546    0.0101757112840443
Delftia 17643   34636   1010    0   412 1.96315819305107    0.015208884326353
Edwardsiella    406 820 26  0   16  2.01970443349754    0.0156469566289747
Enterobacter    11808   16765   512 39  291 1.41980013550135    0.0109994070288449
Enterococcus    47083   80416   2428    0   788 1.70796253424803    0.0132318448452449
Erwinia 6728    14001   431 7   185 2.08100475624257    0.0161218595283423
Escherichia 11306   20159   604 74  231 1.78303555634177    0.0138134469357411
Eubacterium 16623   24962   750 0   254 1.50165433435601    0.0116335439243908
Exiguobacterium 14356   23027   705 0   287 1.60399832822513    0.0124264183701497
Gardnerella 20661   35789   1070    0   299 1.73220076472581    0.0134196220936179
Gordonia    998 2112    64  64  18  2.11623246492986    0.0163947739314729
Haemophilus 2402    3466    109 0   52  1.44296419650291    0.0111788625233376
Klebsiella  54179   80279   2396    384 1150    1.48173646615847    0.0114792371779879
Lactobacillus   36116   55471   1661    65  530 1.53591206113634    0.011898943730545
Lactococcus 33397   53740   1612    258 436 1.60912656825463    0.0124661476235957
Leuconostoc 11985   20703   616 5   163 1.72740926157697    0.0133825015918682
Methylobacterium    40846   69348   2090    371 1144    1.69779170543015    0.0131530498915107
Micrococcus 5068    7254    218 0   101 1.43133385951066    0.0110887605383738
Morganella  12321   18477   531 0   158 1.49963476990504    0.0116178980522276
Mycobacterium   161 407 11  11  4   2.52795031055901    0.0195844145378354
Nocardiopsis    5667    8432    249 0   145 1.48791247573672    0.0115270836610713
Ochrobactrum    11415   19274   563 102 229 1.68848007008322    0.0130809112399329
Oscillatoria    19402   26313   810 63  477 1.35620039171219    0.0105066901658336
Pantoea 19836   30089   924 62  574 1.51688848558177    0.0117515652049085
Parabacteroides 6058    12934   378 0   116 2.13502806206669    0.0165403862737236
Peptoclostridium    407 667 20  0   11  1.63882063882064    0.0126961920927656
Porphyromonas   9467    15395   482 0   245 1.62617513467836    0.012598225453893
Prevotella  6946    12657   388 0   145 1.8221998272387 0.0141168584834736
Propionibacterium   114661  265175  7844    11  3413    2.31268696418137    0.0179167367386903
Pseudomonas 289109  489492  14612   175 6450    1.69310536856341    0.0131167441289019
Psychrobacter   8781    13294   408 93  164 1.51395057510534    0.011728804766776
Raoultella  53687   91392   2712    0   1080    1.70231154655689    0.013188065786365
Rhizobium   12098   23249   687 0   320 1.92172259877666    0.0148878764918627
Rickettsia  406 600 18  0   6   1.47783251231527    0.0114489926553473
Roseburia   5403    8422    255 0   85  1.55876364982417    0.0120759784546221
Rothia  20367   35511   1070    0   443 1.74355575195169    0.0135075909021718
Salmonella  5554    43812   1340    139 395 7.88836874324811    0.0611123892941205
Serratia    4461    6770    208 0   122 1.5175969513562 0.0117570537967349
Shewanella  61821   98671   3011    367 1291    1.59607576713415    0.0123650410875507
Solibacillus    4462    6374    196 0   113 1.42850739578664    0.0110668634951384
Sphingobacterium    41998   68651   2058    0   544 1.63462545835516    0.0126636913933042
Sphingobium 483 681 19  19  7   1.40993788819876    0.0109230027029205
Sphingomonas    1040    2105    64  64  30  2.02403846153846    0.0156805330016658
Sphingopyxis    3461    5210    157 1   103 1.50534527593181    0.0116621382086824
Staphylococcus  36429   59016   1811    45  626 1.62002799967059    0.0125506026664873
Stenotrophomonas    66095   109704  3316    0   1852    1.65979272259626    0.0128586660071731
Streptococcus   21331   35877   1091    0   464 1.68191833481787    0.0130300764814381
Tannerella  3865    5769    170 0   67  1.49262613195343    0.0115636010708287
Unassigned genus - Flavobacteriaceae bacterium 3519-10  6737    9694    292 0   132 1.43891940032655    0.0111475268737767
Unassigned genus - Plautia stali symbiont   4760    6295    195 0   108 1.32247899159664    0.0102454453637104
Veillonella 4607    11541   352 0   143 2.50510093336227    0.0194073969465153
Vibrio  377 671 19  0   8   1.77984084880637    0.0137886970518375
Xanthomonas 277 455 14  0   2   1.64259927797834    0.0127254657835277
Yersinia    516 1427    39  39  16  2.76550387596899    0.0214247780451787
Zymomonas   376 655 20  20  9   1.74202127659574    0.0134957030888143
=================================================================


FAMILY  LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
Aeromonadaceae  11921   18984   573 25  349 1.59248385202584    0.0201468458528872
Akkermansiaceae 4712    8073    233 0   85  1.71328522920204    0.0216751293087535
Alcaligenaceae  22760   35054   1036    0   478 1.54015817223199    0.0194848627479325
Alteromonadaceae    493 911 26  0   5   1.84787018255578    0.0233777916659803
Bacillaceae 20305   33318   1011    18  319 1.64087663137158    0.0207590730127615
Bacteroidaceae  62265   122309  3638    12  1030    1.96432988035012    0.0248511476290888
Bifidobacteriaceae  33086   59676   1775    60  511 1.80366318080155    0.022818519652749
Brucellaceae    11415   19274   563 102 229 1.68848007008322    0.0213613140593949
Carnobacteriaceae   13160   19605   588 96  177 1.48974164133739    0.0188470326844887
Comamonadaceae  84260   184394  5449    0   2153    2.18839306907192    0.0276858178323326
Corynebacteriaceae  14678   27011   821 35  343 1.84023708952173    0.0232812238115923
Enterobacteriaceae  187224  332469  9983    759 4350    1.77578195103192    0.0224657883910517
Enterococcaceae 47083   80416   2428    0   788 1.70796253424803    0.0216077907830762
Eubacteriaceae  16623   24962   750 0   254 1.50165433435601    0.0189977426522123
Flavobacteriaceae   13429   21855   660 0   258 1.62744806016829    0.0205891853534845
Gordoniaceae    998 2112    64  64  18  2.11623246492986    0.0267728989562939
Lachnospiraceae 5403    8422    255 0   85  1.55876364982417    0.0197202445312971
Lactobacillaceae    36116   55471   1661    65  530 1.53591206113634    0.0194311443095261
Leuconostocaceae    11985   20703   616 5   163 1.72740926157697    0.0218538153925823
Methylobacteriaceae 40846   69348   2090    371 1144    1.69779170543015    0.0214791175032001
Micrococcaceae  31012   51889   1564    3   678 1.67319102282987    0.0211678891289889
Moraxellaceae   70299   134237  4114    1760    1728    1.90951507133814    0.0241576740304619
Mycobacteriaceae    161 407 11  11  4   2.52795031055901    0.0319816274217167
Nocardiopsaceae 5667    8432    249 0   145 1.48791247573672    0.0188238915283953
Orobanchaceae   562 807 24  0   9   1.43594306049822    0.0181664156007475
Pasteurellaceae 2402    3466    109 0   52  1.44296419650291    0.0182552414589305
Peptostreptococcaceae   407 667 20  0   11  1.63882063882064    0.0207330622215401
Planococcaceae  4462    6374    196 0   113 1.42850739578664    0.0180723454533063
Porphyromonadaceae  19390   34098   1030    0   428 1.7585353274884 0.0222475977540967
Prevotellaceae  6946    12657   388 0   145 1.8221998272387 0.0230530306387936
Propionibacteriaceae    114661  265175  7844    11  3413    2.31268696418137    0.029258285862096
Pseudomonadaceae    289109  489492  14612   175 6450    1.69310536856341    0.0214198296766085
Rhizobiaceae    12098   23249   687 0   320 1.92172259877666    0.0243121140100169
Rickettsiaceae  406 600 18  0   6   1.47783251231527    0.0186963678056295
Rikenellaceae   4313    5701    165 0   52  1.32181776025968    0.0167225925887306
Shewanellaceae  61821   98671   3011    367 1291    1.59607576713415    0.0201922879212081
Sphingobacteriaceae 41998   68651   2058    0   544 1.63462545835516    0.0206799881171744
Sphingomonadaceae   5360    8651    260 104 149 1.61399253731343    0.0204189567232337
Staphylococcaceae   36429   59016   1811    45  626 1.62002799967059    0.0204953126182124
Streptococcaceae    54728   89617   2703    258 900 1.63749817278176    0.0207163314274431
Unassigned family - Chroococcidiopsis   26595   43232   1291    6   436 1.62556871592405    0.0205654093768897
Unassigned family - Exiguobacterium 14356   23027   705 0   287 1.60399832822513    0.0202925178964491
Unassigned family - Oscillatoria    19402   26313   810 63  477 1.35620039171219    0.0171575744411426
Veillonellaceae 4607    11541   352 0   143 2.50510093336227    0.0316925551779816
Vibrionaceae    377 671 19  0   8   1.77984084880637    0.0225171383546261
Xanthomonadaceae    66372   110159  3330    0   1854    1.65972096667269    0.0209974766348947
=================================================================


ORDER   LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
Aeromonadales   11921   18984   573 25  349 1.59248385202584    0.0345102327754652
Alteromonadales 62314   99582   3037    367 1296    1.59806784992137    0.0346312418939861
Bacillales  75552   121735  3723    63  1345    1.61127435408725    0.0349174360254588
Bacteroidales   92914   174765  5221    12  1655    1.88093290569774    0.0407611244083171
Bifidobacteriales   33086   59676   1775    60  511 1.80366318080155    0.0390866357224372
Burkholderiales 107020  219448  6485    0   2631    2.05053261072697    0.044436467986692
Clostridiales   22433   34051   1025    0   350 1.5178977399367 0.0328938998457852
Corynebacteriales   15837   29530   896 110 365 1.86462082465113    0.0404076302656578
Enterobacteriales   187224  332469  9983    759 4350    1.77578195103192    0.0384824300796659
Flavobacteriales    13429   21855   660 0   258 1.62744806016829    0.0352679314863633
Lactobacillales 163072  265812  7996    424 2558    1.63002845368917    0.0353238504088343
Lamiales    562 807 24  0   9   1.43594306049822    0.0311178849362069
Micrococcales   31012   51889   1564    3   678 1.67319102282987    0.0362592133051914
Oscillatoriales 19402   26313   810 63  477 1.35620039171219    0.0293898058361006
Pasteurellales  2402    3466    109 0   52  1.44296419650291    0.0312700378371999
Pleurocapsales  26595   43232   1291    6   436 1.62556871592405    0.0352272047893536
Propionibacteriales 114661  265175  7844    11  3413    2.31268696418137    0.0501175351757276
Pseudomonadales 359408  623729  18726   1935    8178    1.73543438098206    0.0376080701716683
Rhizobiales 64359   111871  3340    473 1693    1.73823396883109    0.0376687391876978
Rickettsiales   406 600 18  0   6   1.47783251231527    0.0320256584946038
Selenomonadales 4607    11541   352 0   143 2.50510093336227    0.054287279727446
Sphingobacteriales  41998   68651   2058    0   544 1.63462545835516    0.035423470697537
Sphingomonadales    5360    8651    260 104 149 1.61399253731343    0.0349763409466877
Streptosporangiales 5667    8432    249 0   145 1.48791247573672    0.0322440983133811
Verrucomicrobiales  4712    8073    233 0   85  1.71328522920204    0.0371280826460583
Vibrionales 377 671 19  0   8   1.77984084880637    0.0385703892177318
Xanthomonadales 66372   110159  3330    0   1854    1.65972096667269    0.0359673078187455
=================================================================


CLASS   LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
Actinobacteria  200263  414702  12328   184 5112    2.0707869152065 0.08454650932946
Alphaproteobacteria 70125   121122  3618    577 1848    1.72722994652406    0.0705196955396818
Bacilli 238624  387547  11719   487 3903    1.6240906195521 0.0663087021216556
Bacteroidia 92914   174765  5221    12  1655    1.88093290569774    0.076795111216841
Betaproteobacteria  107020  219448  6485    0   2631    2.05053261072697    0.0837195624668611
Clostridia  22433   34051   1025    0   350 1.5178977399367 0.0619730376352735
Flavobacteriia  13429   21855   660 0   258 1.62744806016829    0.0664457803899678
Gammaproteobacteria 690018  1189060 35777   3086    16087   1.7232304084821 0.0703564015870808
Negativicutes   4607    11541   352 0   143 2.50510093336227    0.10227877039325
Sphingobacteriia    41998   68651   2058    0   544 1.63462545835516    0.0667388206628762
Unassigned class - Lamiales 562 807 24  0   9   1.43594306049822    0.0586269753152654
Unassigned class - Oscillatoriales  19402   26313   810 63  477 1.35620039171219    0.055371225416053
Unassigned class - Pleurocapsales   26595   43232   1291    6   436 1.62556871592405    0.0663690501409438
Verrucomicrobiae    4712    8073    233 0   85  1.71328522920204    0.0699503577847898
=================================================================


PHYLUM  LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
Actinobacteria  200263  414702  12328   184 5112    2.0707869152065 0.173803023626757
Bacteroidetes   148341  265271  7939    12  2457    1.78825139374819    0.15008956110156
Cyanobacteria   45997   69545   2101    69  913 1.511946431289  0.126899035043162
Firmicutes  265664  433139  13096   487 4396    1.63040155986509    0.136841081402176
Proteobacteria  867163  1529630 45880   3663    20566   1.76394749314719    0.148049712684826
Streptophyta    562 807 24  0   9   1.43594306049822    0.120520003211225
Verrucomicrobia 4712    8073    233 0   85  1.71328522920204    0.143797582930294
=================================================================
Exporting results to disk [./PAN-0061-QCB_S1.BACTERIA_temp/PAN-0061-QCB_S1.BACTERIA.species.tsv.ABUX]...Done!
Done converting 1 files to list.

----> ENTRY HEADER:@HWI-ST906:483:C5A6FACXX:8:1101:1226:2130#TGGGAGT/1
Threads: 1 (effective)  1 (requested)
IDX = 0: reading from 0 to 170333051204
Staggering at 125000 reads; processed 125000 reads
IDX(0) counted 660331874 reads
GLOBAL READ COUNT = 660331874
Trim Time: 19258233 ms

PROGRAM ELAPSED TIME: 19977773 ms

Parsing HSTEST_temp/splitrim/HSTEST_splitrim.stats.txt... found 1045087807 reads and 36480442110 bases.
->Retrieving parsed DB from disk [/db/GOTTCHA/database/GOTTCHA_VIRUSES_c3498_k85_u24_xHUMAN3x.species.parsedGOTTCHA.dmp]...done.  0 wallclock secs ( 0.03 usr +  0.00 sys =  0.03 CPU)
->Parsing SAM file [-] [main] Version: 0.7.9a-r786
[main] CMD: bwa mem -k 30 -T 0 -B 100 -O 100 -E 100 -t 31 /db/GOTTCHA/database/GOTTCHA_VIRUSES_c3498_k85_u24_xHUMAN3x.species HSTEST_temp/splitrim/HSTEST_splitrim.fastq
[main] Real time: 2.480 sec; CPU: 0.192 sec
done.  1 wallclock secs ( 0.04 usr +  0.00 sys =  0.04 CPU)
->Consolidating hits...done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Retrieving Genome Vitals from disk [/db/GOTTCHA/database/genomeVitals.dmp]...done.  0 wallclock secs ( 0.17 usr +  0.03 sys =  0.20 CPU)
->Storing coordinates to disk [./gottcha//HSTEST_temp/HSTEST.replicon.contig.coords.csv]...done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Storing datastructure GI coordinates to disk in BINARY format as "./gottcha//HSTEST_temp/HSTEST.giCoords.dmp"...done. 0 wallsecs
->Storing datastructure contig length histogram (by entry) to disk in BINARY format as "./gottcha//HSTEST_temp/HSTEST.replicon.contig.HistoByEntry.dmp"...done. 0 wallsecs
->Storing datastructure contig length histogram (by GI) to disk in BINARY format as "./gottcha//HSTEST_temp/HSTEST.replicon.contig.HistoByGI.dmp"...done. 0 wallsecs
->Storing parseable contig length histogram(s) to disk...done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Calculating non-overlapping coverage from mapping results...done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
===== REPLICON-level Analysis =====
->Writing REPLICON-level results to disk [./gottcha//HSTEST_temp/HSTEST.replicon.tsv]...Use of uninitialized value $gis[0] in hash element at /home/x1user/git/gottcha/bin/profileGottcha.pl line 1280.
Use of uninitialized value $gis[0] in hash element at /home/x1user/git/gottcha/bin/profileGottcha.pl line 1281.
done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
===== Extended Taxonomic Rank-level Analysis =====
->Pulling replicon GIs from DB entries...done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Mapping replicon GIs to source organisms...Use of uninitialized value $org in hash element at /home/x1user/git/gottcha/bin/profileGottcha.pl line 1465.
done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Retrieving Tax Tree from disk [/db/GOTTCHA/database/speciesTreeGI.dmp]...done.  6 wallclock secs ( 3.55 usr +  0.58 sys =  4.13 CPU)
->Mapping source organism to its tax tree...done.  1 wallclock secs ( 1.72 usr +  0.04 sys =  1.76 CPU)
->At least one organism name in "/db/GOTTCHA/database/genomeVitals.dmp" is unrecognized in "/db/GOTTCHA/database/speciesTreeGI.dmp":
      []
Continuing on...
->Rolling up results for rank STRAIN [./gottcha//HSTEST_temp/HSTEST.strain.tsv]...TAXTREE does not exist for GI ""!
done.  0 wallclock secs ( 0.21 usr +  0.01 sys =  0.22 CPU)
->Rolling up results for rank SPECIES [./gottcha//HSTEST_temp/HSTEST.species.tsv]...TAXTREE does not exist for GI ""!
done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Rolling up results for rank GENUS [./gottcha//HSTEST_temp/HSTEST.genus.tsv]...TAXTREE does not exist for GI ""!
done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Rolling up results for rank FAMILY [./gottcha//HSTEST_temp/HSTEST.family.tsv]...TAXTREE does not exist for GI ""!
done.  0 wallclock secs ( 0.00 usr +  0.01 sys =  0.01 CPU)
->Rolling up results for rank ORDER [./gottcha//HSTEST_temp/HSTEST.order.tsv]...TAXTREE does not exist for GI ""!
done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Rolling up results for rank CLASS [./gottcha//HSTEST_temp/HSTEST.class.tsv]...TAXTREE does not exist for GI ""!
done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Rolling up results for rank PHYLUM [./gottcha//HSTEST_temp/HSTEST.phylum.tsv]...TAXTREE does not exist for GI ""!
done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
Use of uninitialized value in addition (+) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 516.
Use of uninitialized value in numeric lt (<) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 538.
Saving updated table to "./gottcha//HSTEST_temp/HSTEST.strain.tsv.ABU"...done!
Use of uninitialized value in addition (+) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 516.
Use of uninitialized value in numeric lt (<) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 538.
Saving updated table to "./gottcha//HSTEST_temp/HSTEST.species.tsv.ABU"...done!
Use of uninitialized value in addition (+) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 516.
Use of uninitialized value in numeric lt (<) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 538.
Saving updated table to "./gottcha//HSTEST_temp/HSTEST.genus.tsv.ABU"...done!
Use of uninitialized value in addition (+) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 516.
Use of uninitialized value in numeric lt (<) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 538.
Saving updated table to "./gottcha//HSTEST_temp/HSTEST.family.tsv.ABU"...done!
Use of uninitialized value in addition (+) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 516.
Use of uninitialized value in numeric lt (<) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 538.
Saving updated table to "./gottcha//HSTEST_temp/HSTEST.order.tsv.ABU"...done!
Use of uninitialized value in addition (+) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 516.
Use of uninitialized value in numeric lt (<) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 538.
Saving updated table to "./gottcha//HSTEST_temp/HSTEST.class.tsv.ABU"...done!
Use of uninitialized value in addition (+) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 516.
Use of uninitialized value in numeric lt (<) at /home/x1user/git/gottcha/bin/profileGottcha.pl line 538.
Saving updated table to "./gottcha//HSTEST_temp/HSTEST.phylum.tsv.ABU"...done!
------------------
TOTAL SCRIPT TIME:  -   10 wallclock secs ( 6.98 usr +  0.67 sys =  7.65 CPU)
------------------
Done converting 1 files to list.
Done converting 7 files to list.

----> ENTRY HEADER:@M70116:4:000000000-AJEH6:1:1101:14371:1905 1:N:0:7
Threads: 1 (effective)  1 (requested)
IDX = 0: reading from 0 to 1920571466
Staggering at 125000 reads; processed 125000 reads
IDX(0) counted 5534518 reads
GLOBAL READ COUNT = 5534518
Trim Time: 281203 ms

PROGRAM ELAPSED TIME: 298459 ms
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 4173880 sequences (140000054 bp)...
[M::process] read 4161872 sequences (140000050 bp)...
[M::mem_process_seqs] Processed 4173880 reads in 179.171 CPU sec, 17.148 real sec
[M::mem_process_seqs] Processed 4161872 reads in 170.680 CPU sec, 14.698 real sec
[M::process] read 4108872 sequences (140000067 bp)...
[M::mem_process_seqs] Processed 4108872 reads in 162.569 CPU sec, 12.050 real sec
[M::process] read 4110420 sequences (140000064 bp)...
[M::mem_process_seqs] Processed 4110420 reads in 162.380 CPU sec, 11.671 real sec
[M::process] read 683426 sequences (23120420 bp)...
[M::mem_process_seqs] Processed 683426 reads in 26.500 CPU sec, 2.061 real sec
[main] Version: 0.7.12-r1044
[main] CMD: bwa mem -k 30 -T 0 -B 100 -O 100 -E 100 -t 14 /home/src/gottcha/database/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species -
[main] Real time: 154.603 sec; CPU: 751.777 sec

Parsing ./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA_splitrim.stats.txt... found 5534518 reads (split-trimmed: 17238470) and 579914609 bases.
->Retrieving parsed DB from disk [/home/src/gottcha/database/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.parsedGOTTCHA.dmp]...done. 16 wallclock secs (14.02 usr +  2.05 sys = 16.07 CPU)
->Parsing SAM file [-] done. Mapped split-trimmed reads: 170; Mapped split-trimmed reads to plasmids: 14; Unmapped split-trimmed reads: 17238259; Mapped raw reads: 59; Mapped raw reads to plasmids: 6. 139 wallclock secs (100.16 usr +  1.82 sys = 101.98 CPU)
->Consolidating hits...done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Retrieving Genome Vitals from disk [/home/src/gottcha/database/genomeVitals.dmp]...done.  0 wallclock secs ( 0.19 usr +  0.03 sys =  0.22 CPU)
->Storing coordinates to disk [./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.replicon.contig.coords.csv]...done.  0 wallclock secs ( 0.01 usr +  0.00 sys =  0.01 CPU)
->Storing datastructure GI coordinates to disk in BINARY format as "./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.giCoords.dmp"...done. 0 wallsecs
->Storing datastructure contig length histogram (by entry) to disk in BINARY format as "./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.replicon.contig.HistoByEntry.dmp"...done. 0 wallsecs
->Storing datastructure contig length histogram (by GI) to disk in BINARY format as "./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.replicon.contig.HistoByGI.dmp"...done. 0 wallsecs
->Storing parseable contig length histogram(s) to disk...done.  1 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Calculating non-overlapping coverage from mapping results...done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
===== REPLICON-level Analysis =====
->Writing REPLICON-level results to disk [./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.replicon.tsv]...done.  1 wallclock secs ( 0.08 usr +  0.00 sys =  0.08 CPU)
===== Extended Taxonomic Rank-level Analysis =====
->Pulling replicon GIs from DB entries...done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Mapping replicon GIs to source organisms...done.  0 wallclock secs ( 0.00 usr +  0.00 sys =  0.00 CPU)
->Retrieving Tax Tree from disk [/home/src/gottcha/database/speciesTreeGI.dmp]...done.  5 wallclock secs ( 5.56 usr +  0.14 sys =  5.70 CPU)
->Mapping source organism to its tax tree...done.  3 wallclock secs ( 2.96 usr +  0.01 sys =  2.97 CPU)
  Congratulations! All organisms have been identified!
->Rolling up results for rank STRAIN [./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.strain.tsv]...done.  1 wallclock secs ( 0.70 usr +  0.00 sys =  0.70 CPU)
->Rolling up results for rank SPECIES [./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.species.tsv]...done.  1 wallclock secs ( 0.24 usr +  0.00 sys =  0.24 CPU)
->Rolling up results for rank GENUS [./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.genus.tsv]...done.  0 wallclock secs ( 0.24 usr +  0.00 sys =  0.24 CPU)
->Rolling up results for rank FAMILY [./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.family.tsv]...done.  1 wallclock secs ( 0.23 usr +  0.00 sys =  0.23 CPU)
->Rolling up results for rank ORDER [./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.order.tsv]...done.  0 wallclock secs ( 0.24 usr +  0.01 sys =  0.25 CPU)
->Rolling up results for rank CLASS [./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.class.tsv]...done.  1 wallclock secs ( 0.23 usr +  0.00 sys =  0.23 CPU)
->Rolling up results for rank PHYLUM [./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.phylum.tsv]...done.  0 wallclock secs ( 0.24 usr +  0.00 sys =  0.24 CPU)
Saving updated table to "./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.strain.tsv.ABU"...done. (20 taxonomie(s), 20 filtered)
Saving updated table to "./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.species.tsv.ABU"...done. (18 taxonomie(s), 18 filtered)
Saving updated table to "./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.genus.tsv.ABU"...done. (13 taxonomie(s), 13 filtered)
Saving updated table to "./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.family.tsv.ABU"...done. (10 taxonomie(s), 10 filtered)
Saving updated table to "./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.order.tsv.ABU"...done. (7 taxonomie(s), 7 filtered)
Saving updated table to "./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.class.tsv.ABU"...done. (5 taxonomie(s), 5 filtered)
Saving updated table to "./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.phylum.tsv.ABU"...done. (3 taxonomie(s), 3 filtered)
------------------
TOTAL SCRIPT TIME:  -   177 wallclock secs (132.39 usr +  4.08 sys = 136.47 CPU)
------------------
Loading STRAIN Lookup file...done!
Loading SPECIES Lookup file...done!
Loading GENUS Lookup file...done!
Loading FAMILY Lookup file...done!
Loading ORDER Lookup file...done!
Loading CLASS Lookup file...done!
Loading PHYLUM Lookup file...done!
Loading TAX Lookup file...done!
Parsing table "./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.strain.tsv"...Done!


STRAIN  LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
=================================================================


SPECIES LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
=================================================================


GENUS   LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
=================================================================


FAMILY  LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
=================================================================


ORDER   LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
=================================================================


CLASS   LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
=================================================================


PHYLUM  LINEAR_LENGTH   TOTAL_BP_MAPPED HIT_COUNT   HIT_COUNT_PLASMID   READ_COUNT  LINEAR_DOC  NORM_COV
=================================================================
Exporting results to disk [./PAN-0060-QCB_S7.BACTERIA_temp/PAN-0060-QCB_S7.BACTERIA.species.tsv.ABUX]...Done!