[2024-01-24 13:57:01,182] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:01,186] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:01,186] [INFO] DQC Reference Directory: /var/lib/cwl/stg0062653f-f318-4c03-a79e-d8228a9e4957/dqc_reference
[2024-01-24 13:57:02,672] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,673] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,674] [INFO] Running command: gunzip -c /var/lib/cwl/stge09d41fc-71e5-43cb-ac74-07a4b57c057f/GCF_006409125.1_ASM640912v1_genomic.fna.gz | prodigal -d GCF_006409125.1_ASM640912v1_genomic.fna/cds.fna -a GCF_006409125.1_ASM640912v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:21,024] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:21,025] [INFO] Task started: HMMsearch
[2024-01-24 13:57:21,025] [INFO] Running command: hmmsearch --tblout GCF_006409125.1_ASM640912v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0062653f-f318-4c03-a79e-d8228a9e4957/dqc_reference/reference_markers.hmm GCF_006409125.1_ASM640912v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:21,385] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:21,387] [INFO] Found 6/6 markers.
[2024-01-24 13:57:21,433] [INFO] Query marker FASTA was written to GCF_006409125.1_ASM640912v1_genomic.fna/markers.fasta
[2024-01-24 13:57:21,433] [INFO] Task started: Blastn
[2024-01-24 13:57:21,433] [INFO] Running command: blastn -query GCF_006409125.1_ASM640912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0062653f-f318-4c03-a79e-d8228a9e4957/dqc_reference/reference_markers.fasta -out GCF_006409125.1_ASM640912v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:22,552] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:22,557] [INFO] Selected 5 target genomes.
[2024-01-24 13:57:22,557] [INFO] Target genome list was writen to GCF_006409125.1_ASM640912v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:22,561] [INFO] Task started: fastANI
[2024-01-24 13:57:22,561] [INFO] Running command: fastANI --query /var/lib/cwl/stge09d41fc-71e5-43cb-ac74-07a4b57c057f/GCF_006409125.1_ASM640912v1_genomic.fna.gz --refList GCF_006409125.1_ASM640912v1_genomic.fna/target_genomes.txt --output GCF_006409125.1_ASM640912v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:28,738] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:28,738] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0062653f-f318-4c03-a79e-d8228a9e4957/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:28,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0062653f-f318-4c03-a79e-d8228a9e4957/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:28,745] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:57:28,745] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:28,745] [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
Mycobacteroides abscessus subsp. bolletii	strain=CCUG 50184	GCA_006409125.1	319705	36809	type	True	100.0	1668	1670	95	conclusive
Mycobacteroides abscessus subsp. bolletii	strain=BD	GCA_003609715.1	319705	36809	type	True	99.9957	1668	1670	95	conclusive
Mycobacteroides abscessus subsp. bolletii	strain=CIP108541	GCA_002086525.1	319705	36809	type	True	99.9898	1652	1670	95	conclusive
Mycobacteroides abscessus subsp. bolletii	strain=CIP 108541	GCA_001792615.1	319705	36809	type	True	99.984	1615	1670	95	conclusive
Mycobacteroides abscessus subsp. bolletii	strain=BD	GCA_000239035.2	319705	36809	type	True	99.975	1651	1670	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:57:28,747] [INFO] DFAST Taxonomy check result was written to GCF_006409125.1_ASM640912v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:28,748] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:28,748] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:28,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0062653f-f318-4c03-a79e-d8228a9e4957/dqc_reference/checkm_data
[2024-01-24 13:57:28,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:28,801] [INFO] Task started: CheckM
[2024-01-24 13:57:28,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006409125.1_ASM640912v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006409125.1_ASM640912v1_genomic.fna/checkm_input GCF_006409125.1_ASM640912v1_genomic.fna/checkm_result
[2024-01-24 13:58:21,008] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:21,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:21,030] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:21,030] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:21,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006409125.1_ASM640912v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:21,031] [INFO] Task started: Blastn
[2024-01-24 13:58:21,031] [INFO] Running command: blastn -query GCF_006409125.1_ASM640912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0062653f-f318-4c03-a79e-d8228a9e4957/dqc_reference/reference_markers_gtdb.fasta -out GCF_006409125.1_ASM640912v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:22,685] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:22,689] [INFO] Selected 8 target genomes.
[2024-01-24 13:58:22,689] [INFO] Target genome list was writen to GCF_006409125.1_ASM640912v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:22,702] [INFO] Task started: fastANI
[2024-01-24 13:58:22,702] [INFO] Running command: fastANI --query /var/lib/cwl/stge09d41fc-71e5-43cb-ac74-07a4b57c057f/GCF_006409125.1_ASM640912v1_genomic.fna.gz --refList GCF_006409125.1_ASM640912v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006409125.1_ASM640912v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:32,616] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:32,624] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:32,624] [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
GCA_000069185.1	s__Mycobacterium abscessus	97.2167	1503	1670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	96.83	0.93	0.86	1820	conclusive
GCF_001605725.1	s__Mycobacterium immunogenum	86.3435	1348	1670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.78	96.59	0.98	0.90	18	-
GCF_002013895.1	s__Mycobacterium franklinii	85.85	1350	1670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.20	95.66	0.94	0.87	12	-
GCF_001456355.1	s__Mycobacterium saopaulense	85.1565	1300	1670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.82	98.51	0.95	0.95	4	-
GCF_014204435.1	s__Mycobacterium chelonae_A	84.6763	1069	1670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632805.1	s__Mycobacterium chelonae	83.9562	1260	1670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.73	95.27	0.90	0.84	73	-
GCF_002356335.1	s__Mycobacterium stephanolepidis	83.8897	1252	1670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013449725.1	s__Mycobacterium sp013449725	82.9954	1220	1670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:32,626] [INFO] GTDB search result was written to GCF_006409125.1_ASM640912v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:32,626] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:32,629] [INFO] DFAST_QC result json was written to GCF_006409125.1_ASM640912v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:32,629] [INFO] DFAST_QC completed!
[2024-01-24 13:58:32,630] [INFO] Total running time: 0h1m31s