[2024-01-24 13:49:32,070] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:32,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:32,083] [INFO] DQC Reference Directory: /var/lib/cwl/stgccfc348f-7f71-4a2d-bbc6-f79b2bca0d66/dqc_reference
[2024-01-24 13:49:33,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:33,423] [INFO] Task started: Prodigal
[2024-01-24 13:49:33,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg088bc9ab-bcd6-4229-a3f0-258f2182d52b/GCF_018596335.1_ASM1859633v1_genomic.fna.gz | prodigal -d GCF_018596335.1_ASM1859633v1_genomic.fna/cds.fna -a GCF_018596335.1_ASM1859633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:47,012] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:47,012] [INFO] Task started: HMMsearch
[2024-01-24 13:49:47,013] [INFO] Running command: hmmsearch --tblout GCF_018596335.1_ASM1859633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccfc348f-7f71-4a2d-bbc6-f79b2bca0d66/dqc_reference/reference_markers.hmm GCF_018596335.1_ASM1859633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:47,327] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:47,328] [INFO] Found 6/6 markers.
[2024-01-24 13:49:47,366] [INFO] Query marker FASTA was written to GCF_018596335.1_ASM1859633v1_genomic.fna/markers.fasta
[2024-01-24 13:49:47,366] [INFO] Task started: Blastn
[2024-01-24 13:49:47,367] [INFO] Running command: blastn -query GCF_018596335.1_ASM1859633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccfc348f-7f71-4a2d-bbc6-f79b2bca0d66/dqc_reference/reference_markers.fasta -out GCF_018596335.1_ASM1859633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:48,294] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:48,298] [INFO] Selected 8 target genomes.
[2024-01-24 13:49:48,299] [INFO] Target genome list was writen to GCF_018596335.1_ASM1859633v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:48,309] [INFO] Task started: fastANI
[2024-01-24 13:49:48,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg088bc9ab-bcd6-4229-a3f0-258f2182d52b/GCF_018596335.1_ASM1859633v1_genomic.fna.gz --refList GCF_018596335.1_ASM1859633v1_genomic.fna/target_genomes.txt --output GCF_018596335.1_ASM1859633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:55,754] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:55,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccfc348f-7f71-4a2d-bbc6-f79b2bca0d66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:55,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccfc348f-7f71-4a2d-bbc6-f79b2bca0d66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:55,762] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:55,763] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:55,763] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	100.0	1464	1465	95	conclusive
Shewanella khirikhana	strain=TH2012	GCA_003957745.1	1965282	1965282	type	True	83.8167	1131	1465	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	82.5143	914	1465	95	below_threshold
Shewanella litorisediminis	strain=SMK1-12	GCA_016834455.1	1173586	1173586	type	True	82.472	919	1465	95	below_threshold
Shewanella amazonensis	strain=SB2B	GCA_000015245.1	60478	60478	type	True	82.173	885	1465	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	77.804	344	1465	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.7547	77	1465	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.6304	77	1465	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:55,764] [INFO] DFAST Taxonomy check result was written to GCF_018596335.1_ASM1859633v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:55,765] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:55,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:55,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccfc348f-7f71-4a2d-bbc6-f79b2bca0d66/dqc_reference/checkm_data
[2024-01-24 13:49:55,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:55,819] [INFO] Task started: CheckM
[2024-01-24 13:49:55,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018596335.1_ASM1859633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018596335.1_ASM1859633v1_genomic.fna/checkm_input GCF_018596335.1_ASM1859633v1_genomic.fna/checkm_result
[2024-01-24 13:50:38,658] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:38,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:38,676] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:38,677] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:38,677] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018596335.1_ASM1859633v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:38,677] [INFO] Task started: Blastn
[2024-01-24 13:50:38,678] [INFO] Running command: blastn -query GCF_018596335.1_ASM1859633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccfc348f-7f71-4a2d-bbc6-f79b2bca0d66/dqc_reference/reference_markers_gtdb.fasta -out GCF_018596335.1_ASM1859633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:40,133] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:40,136] [INFO] Selected 6 target genomes.
[2024-01-24 13:50:40,136] [INFO] Target genome list was writen to GCF_018596335.1_ASM1859633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:40,141] [INFO] Task started: fastANI
[2024-01-24 13:50:40,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg088bc9ab-bcd6-4229-a3f0-258f2182d52b/GCF_018596335.1_ASM1859633v1_genomic.fna.gz --refList GCF_018596335.1_ASM1859633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018596335.1_ASM1859633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:46,043] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:46,049] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:46,049] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_018596335.1	s__Shewanella sp018596335	100.0	1464	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003957745.1	s__Shewanella khirikhana	83.8086	1132	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016834455.1	s__Shewanella litorisediminis	82.4706	919	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015245.1	s__Shewanella amazonensis	82.1617	888	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017354985.1	s__Shewanella sp017354985	79.6882	562	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_000014665.1	s__Shewanella sp000014665	77.9774	348	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:46,051] [INFO] GTDB search result was written to GCF_018596335.1_ASM1859633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:46,051] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:46,054] [INFO] DFAST_QC result json was written to GCF_018596335.1_ASM1859633v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:46,054] [INFO] DFAST_QC completed!
[2024-01-24 13:50:46,054] [INFO] Total running time: 0h1m14s