bodeolukolu / qmatey Goto Github PK

#General_parameters
####################################################
threads=24
cluster=false
samples_alt_dir=false
library_type=WGS
HDsubsample=false
subsample_shotgun_R1=true
subsample_shotgun_R2=true
shotgun_min_read_length=100

#simulation_parameters
####################################################
simulation_lib=complete_digest
simulation_motif_R1=ATGCAT
simulation_motif_R2=CATG
fragment_size_range=64,600
max_read_length=150
gcov=3

#Normalization
####################################################
normalization=true

#MegaBLAST
####################################################
blast_location=custom
local_db=
#local_db=/media/sdd/ncbi_db/nt/nr
#local_db=/media/sdb/ncbi_db/16S/16S_ribosomal_RNA,/media/sdb/ncbi_db/18S/18S_fungal_sequences,/media/sdb/ncbi_db/28S/28S_fungal_sequences,/media/sdb/ncbi_db/ITS/ITS_eukaryote_sequences
#local_db=/media/sdd/ncbi_db/refseq/refseq_rna,/media/sdd/ncbi_db/refseq/ref_viroids_rep_genomes,/media/sdd/ncbi_db/refseq/ref_prok_rep_genomes,/media/sdd/ncbi_db/refseq/ref_euk_rep_genomes
taxids=true
input_dbfasta=/home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/db/reference_genomes.fa
map_taxids=/home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/taxids/seqid2taxid.map

#Taxonomic_Profiling_and_Filtering
####################################################
taxonomic_level=species
spearman_corr=species
CCLasso_corr=
min_percent_sample=10,20
min_pos_corr=0.1,0.2,0.3
max_neg_corr=0.1,0.2,0.3

#Visualizations
####################################################
sunburst_taxlevel=species
sunburst_nlayers=species


#Advanced_Parameters
####################################################
nodes=1
minRD=0
fullqlen_alignment=false
reads_per_megablast=10000
reads_per_megablast_burn_in=10000
zero_inflated=0.01
exclude_rRNA=false
annotate_seq=false

- only paired-end reads available in pe-folder 

ls: cannot access '*_R2.fasta.gz': No such file or directory
ls: cannot access '*.R2.fasta.gz': No such file or directory
cat: sample.fq.tmp1.txt: No such file or directory
rm: cannot remove 'sample.fq.tmp1.txt': No such file or directory
 �[31m normalization reference folder is empty, Qmatey will not exclude any read
 �[31m Qmatey will use read coverage of samples for normalization
- calculating a normalization factor
- compile metagenome reads & compute relative read depth �[97m
cat: '/home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/taxids/*.txids': No such file or directory
- performing custom BLAST
USAGE
  blastn [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-task task_name] [-db database_name]
    [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
    [-negative_gilist filename] [-negative_seqidlist filename]
    [-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
    [-negative_taxidlist filename] [-entrez_query entrez_query]
    [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
    [-subject subject_input_file] [-subject_loc range] [-query input_file]
    [-out output_file] [-evalue evalue] [-word_size int_value]
    [-gapopen open_penalty] [-gapextend extend_penalty]
    [-perc_identity float_value] [-qcov_hsp_perc float_value]
    [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
    [-xdrop_gap_final float_value] [-searchsp int_value] [-penalty penalty]
    [-reward reward] [-no_greedy] [-min_raw_gapped_score int_value]
    [-template_type type] [-template_length int_value] [-dust DUST_options]
    [-filtering_db filtering_database]
    [-window_masker_taxid window_masker_taxid]
    [-window_masker_db window_masker_db] [-soft_masking soft_masking]
    [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
    [-best_hit_score_edge float_value] [-subject_besthit]
    [-window_size int_value] [-off_diagonal_range int_value]
    [-use_index boolean] [-index_name string] [-lcase_masking]
    [-query_loc range] [-strand strand] [-parse_deflines] [-outfmt format]
    [-show_gis] [-num_descriptions int_value] [-num_alignments int_value]
    [-line_length line_length] [-html] [-sorthits sort_hits]
    [-sorthsps sort_hsps] [-max_target_seqs num_sequences]
    [-num_threads int_value] [-mt_mode int_value] [-remote] [-version]

DESCRIPTION
   Nucleotide-Nucleotide BLAST 2.14.0+

Use '-help' to print detailed descriptions of command line arguments
========================================================================

Error: Too many positional arguments (1), the offending value: wait
Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: wait
gzip: subfileF1_1_out.blast: No such file or directory
cat: '*_out.blast.gz': No such file or directory
ls: cannot access '*subfile*': No such file or directory

gzip: /home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/metagenome/alignment/combined_compressed.megablast.gz: unexpected end of file

gzip: /home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/metagenome/alignment/combined_compressed.megablast.gz: unexpected end of file
awk: fatal: cannot open file `/home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/taxids/*.txids' for reading (No such file or directory)
awk: fatal: cannot open file `/home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/taxids/*.txids' for reading (No such file or directory)
- performing cross-taxon validation and filtering at class level
/home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/Qmatey_run.sh: line 6110: cd: /home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/metagenome/results/class_level: No such file or directory

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Error in file(file, "rt") : cannot open the connection
Calls: read.delim -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '../phylum_level/phylum_taxainfo_unique_sequences.txt': No such file or directory
Execution halted
- performing cross-taxon validation and filtering at order level
/home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/Qmatey_run.sh: line 6117: cd: /home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/metagenome/results/order_level: No such file or directory

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Error in file(file, "rt") : cannot open the connection
Calls: read.delim -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '../class_level_validated/class_taxainfo_unique_sequences.txt': No such file or directory
Execution halted
- performing cross-taxon validation and filtering at family level
/home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/Qmatey_run.sh: line 6124: cd: /home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/metagenome/results/family_level: No such file or directory

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Error in file(file, "rt") : cannot open the connection
Calls: read.delim -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '../order_level_validated/order_taxainfo_unique_sequences.txt': No such file or directory
Execution halted
- performing cross-taxon validation and filtering at genus level
/home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/Qmatey_run.sh: line 6131: cd: /home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/metagenome/results/genus_level: No such file or directory

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Error in file(file, "rt") : cannot open the connection
Calls: read.delim -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '../family_level_validated/family_taxainfo_unique_sequences.txt': No such file or directory
Execution halted
- performing cross-taxon validation and filtering at species level

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Error in file(file, "rt") : cannot open the connection
Calls: read.delim -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '../genus_level_validated/genus_taxainfo_unique_sequences.txt': No such file or directory
Execution halted
- performing cross-taxon validation and filtering at strain level (mininimum unique seqeuence = 1)
/home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/Qmatey_run.sh: line 6145: cd: /home/work/wenhai/metaprofiling/bacteria_refgenome_NCBIdata/pggb_vg/big_sample/alternative_methods/Qmatey/Qmatey/metagenome/results/strain_level_minUniq_1: No such file or directory

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Error in file(file, "rt") : cannot open the connection
Calls: read.delim -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '../species_level_validated/species_taxainfo_unique_sequences.txt': No such file or directory
Execution halted

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Error in file(file, "rt") : cannot open the connection
Calls: read.delim -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file './phylum_level/phylum_taxainfo_unique_sequences.txt': No such file or directory
Execution halted
�[97m########################################################
 �[38;5;210mQmatey is creating sunburst 
�[97m########################################################

- creating sunburst from species_level taxonomic profile