[2024-01-24 12:46:57,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:57,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:57,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg825eb716-1f25-44a6-bb42-26eb17540519/dqc_reference
[2024-01-24 12:46:59,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:59,091] [INFO] Task started: Prodigal
[2024-01-24 12:46:59,091] [INFO] Running command: gunzip -c /var/lib/cwl/stgd905f357-e598-4695-ac48-a3174792854a/GCF_000497265.2_ASM49726v2_genomic.fna.gz | prodigal -d GCF_000497265.2_ASM49726v2_genomic.fna/cds.fna -a GCF_000497265.2_ASM49726v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:23,459] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:23,459] [INFO] Task started: HMMsearch
[2024-01-24 12:47:23,459] [INFO] Running command: hmmsearch --tblout GCF_000497265.2_ASM49726v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg825eb716-1f25-44a6-bb42-26eb17540519/dqc_reference/reference_markers.hmm GCF_000497265.2_ASM49726v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:23,749] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:23,750] [INFO] Found 6/6 markers.
[2024-01-24 12:47:23,798] [INFO] Query marker FASTA was written to GCF_000497265.2_ASM49726v2_genomic.fna/markers.fasta
[2024-01-24 12:47:23,799] [INFO] Task started: Blastn
[2024-01-24 12:47:23,799] [INFO] Running command: blastn -query GCF_000497265.2_ASM49726v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg825eb716-1f25-44a6-bb42-26eb17540519/dqc_reference/reference_markers.fasta -out GCF_000497265.2_ASM49726v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:24,845] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:24,848] [INFO] Selected 5 target genomes.
[2024-01-24 12:47:24,849] [INFO] Target genome list was writen to GCF_000497265.2_ASM49726v2_genomic.fna/target_genomes.txt
[2024-01-24 12:47:24,856] [INFO] Task started: fastANI
[2024-01-24 12:47:24,856] [INFO] Running command: fastANI --query /var/lib/cwl/stgd905f357-e598-4695-ac48-a3174792854a/GCF_000497265.2_ASM49726v2_genomic.fna.gz --refList GCF_000497265.2_ASM49726v2_genomic.fna/target_genomes.txt --output GCF_000497265.2_ASM49726v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:30,984] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:30,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg825eb716-1f25-44a6-bb42-26eb17540519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:30,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg825eb716-1f25-44a6-bb42-26eb17540519/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:30,991] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:47:30,991] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:30,991] [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. massiliense	strain=JCM 15300	GCA_000497265.2	1962118	36809	type	True	100.0	1659	1659	95	conclusive
Mycobacteroides abscessus subsp. massiliense	strain=CCUG 48898	GCA_002086375.1	1962118	36809	type	True	99.9941	1638	1659	95	conclusive
Mycobacteroides abscessus subsp. massiliense	strain=CCUG 48898	GCA_000270665.1	1962118	36809	type	True	99.9937	1653	1659	95	conclusive
Mycobacteroides abscessus subsp. massiliense	strain=CCUG 48898	GCA_000239055.2	1962118	36809	type	True	99.9858	1643	1659	95	conclusive
Mycobacteroides abscessus subsp. massiliense	strain=CIP 108297	GCA_001792625.1	1962118	36809	type	True	99.9698	1584	1659	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:47:30,993] [INFO] DFAST Taxonomy check result was written to GCF_000497265.2_ASM49726v2_genomic.fna/tc_result.tsv
[2024-01-24 12:47:30,994] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:30,994] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:30,994] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg825eb716-1f25-44a6-bb42-26eb17540519/dqc_reference/checkm_data
[2024-01-24 12:47:30,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:31,043] [INFO] Task started: CheckM
[2024-01-24 12:47:31,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000497265.2_ASM49726v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000497265.2_ASM49726v2_genomic.fna/checkm_input GCF_000497265.2_ASM49726v2_genomic.fna/checkm_result
[2024-01-24 12:48:38,405] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:38,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:38,428] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:38,429] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:38,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000497265.2_ASM49726v2_genomic.fna/markers.fasta)
[2024-01-24 12:48:38,430] [INFO] Task started: Blastn
[2024-01-24 12:48:38,430] [INFO] Running command: blastn -query GCF_000497265.2_ASM49726v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg825eb716-1f25-44a6-bb42-26eb17540519/dqc_reference/reference_markers_gtdb.fasta -out GCF_000497265.2_ASM49726v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:39,947] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:39,951] [INFO] Selected 8 target genomes.
[2024-01-24 12:48:39,952] [INFO] Target genome list was writen to GCF_000497265.2_ASM49726v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:39,959] [INFO] Task started: fastANI
[2024-01-24 12:48:39,959] [INFO] Running command: fastANI --query /var/lib/cwl/stgd905f357-e598-4695-ac48-a3174792854a/GCF_000497265.2_ASM49726v2_genomic.fna.gz --refList GCF_000497265.2_ASM49726v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000497265.2_ASM49726v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:49,757] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:49,772] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:49,773] [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	96.9159	1497	1659	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	86.424	1355	1659	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	85.8366	1357	1659	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	85.383	1296	1659	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	84.7774	1073	1659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356335.1	s__Mycobacterium stephanolepidis	83.8141	1254	1659	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	83.0469	1218	1659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001666835.1	s__Mycobacterium sp001666835	77.6812	360	1659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:49,775] [INFO] GTDB search result was written to GCF_000497265.2_ASM49726v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:49,775] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:49,780] [INFO] DFAST_QC result json was written to GCF_000497265.2_ASM49726v2_genomic.fna/dqc_result.json
[2024-01-24 12:48:49,780] [INFO] DFAST_QC completed!
[2024-01-24 12:48:49,780] [INFO] Total running time: 0h1m52s