dulunar / chimeraminer Goto Github PK

perl AlignReadstoRef.pl -fq ./fastq.ls -ref /Analysis/mcospino/ChimeraMiner/index_fasta/combined.fasta -hdir /Analysis/mcospino/ChimeraMiner/test1 -sh work -dh no

perl /Analysis/mcospino/ChimeraMiner/Generate_Shell_Finder.pl \
-i bam.lst -o runFinder.Test.sh \
-S1 /Analysis/mcospino/ChimeraMiner/Insertion.SRExtract.ReConFastq.pl \
-S2 /Analysis/mcospino/ChimeraMiner/SearchOverlapSEchimera.pl \
-L 20 \
-r /Analysis/mcospino/ChimeraMiner/index_fasta/combined.fasta

/Analysis/mcospino/ChimeraMiner/Insertion.SRExtract.ReConFastq.pl  \
-i /Analysis/mcospino/ChimeraMiner/test1/Test/Test.mem.bam  \
-m Test -d /Analysis/mcospino/ChimeraMiner/test1/Test  \
-r /Analysis/mcospino/ChimeraMiner/index_fasta/combined.fasta  \
-g BS.pilon.polished.v3.ST170922","Enterococcus_faecalis_complete_genome","scherichia_coli_plasmid","Escherichia_coli_chromosome","Lactobacillus_fermentum_complete_genome","Listeria_monocytogenes_complete_genome","Pseudomonas_aeruginosa_complete_genome","Salmonella_enterica_plasmid1","Salmonella_enterica_chromosome","Staphylococcus_aureus_chromosome","Staphylococcus_aureus_plasmid1","Staphylococcus_aureus_plasmid2","Staphylococcus_aureus_plasmid3"  \
-L 4045677,2845388,110007,4765434,1905333,2992342,6792330,49572,4759744,2718780,6337,2216,2993

bwa mem -t 20 -k 30 -R '@RG\tID:Test\tLB:Test\tSM:Test\tPL:ILLUMINA' $ref Test/test_R1.fq.gz Test/test_R2.fq.gz | awk '$6 !~ /H/' | samtools view -Sb -t ${ref}.fai -o $dir/Test/Test.dh.bam -
echo -e "Test\t$dir/Test/Test.dh.bam" > bam.lst
perl Generate_Shell_Finder.pl -i bam.lst -o runFinder.Test.sh -L 20 -r $ref
bash runFinder.Test.sh

Tue Feb 16 17:35:34 UTC 2021
###Test start
Use of uninitialized value in addition (+) at /home/simone/software/ChimeraMiner/Insertion.SRExtract.ReConFastq.pl line 224, <IN> line 68.
Use of uninitialized value in addition (+) at /home/simone/software/ChimeraMiner/Insertion.SRExtract.ReConFastq.pl line 224, <IN> line 264.
Can't use an undefined value as a symbol reference at /home/simone/software/ChimeraMiner/Insertion.SRExtract.ReConFastq.pl line 301, <IN> line 264.
Tue Feb 16 17:35:35 UTC 2021

# packages in environment at /home/simone/miniconda3/envs/ChimeraMiner_env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
bwa                       0.7.17               hed695b0_7    bioconda
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h36c2ea0_0    conda-forge
ca-certificates           2020.12.5            ha878542_0    conda-forge
htslib                    1.11                 hd3b49d5_2    bioconda
krb5                      1.17.2               h926e7f8_0    conda-forge
libcurl                   7.71.1               hcdd3856_8    conda-forge
libdeflate                1.7                  h7f98852_5    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libgcc-ng                 9.3.0               h2828fa1_18    conda-forge
libgomp                   9.3.0               h2828fa1_18    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libssh2                   1.9.0                hab1572f_5    conda-forge
libstdcxx-ng              9.3.0               h6de172a_18    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
openssl                   1.1.1i               h7f98852_0    conda-forge
perl                      5.32.0               h36c2ea0_0    conda-forge
samtools                  1.11                 h6270b1f_0    bioconda
tk                        8.6.10               h21135ba_1    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge