[2024-01-24 11:20:49,990] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:49,993] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:49,993] [INFO] DQC Reference Directory: /var/lib/cwl/stga68d7a7e-c376-4d8c-8e80-aefa0394763e/dqc_reference
[2024-01-24 11:20:51,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:51,239] [INFO] Task started: Prodigal
[2024-01-24 11:20:51,240] [INFO] Running command: gunzip -c /var/lib/cwl/stg679b91f7-5715-4c29-84e8-1f78bdf0e328/GCF_025821785.1_ASM2582178v1_genomic.fna.gz | prodigal -d GCF_025821785.1_ASM2582178v1_genomic.fna/cds.fna -a GCF_025821785.1_ASM2582178v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:11,012] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:11,012] [INFO] Task started: HMMsearch
[2024-01-24 11:21:11,013] [INFO] Running command: hmmsearch --tblout GCF_025821785.1_ASM2582178v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga68d7a7e-c376-4d8c-8e80-aefa0394763e/dqc_reference/reference_markers.hmm GCF_025821785.1_ASM2582178v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:11,305] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:11,307] [INFO] Found 6/6 markers.
[2024-01-24 11:21:11,363] [INFO] Query marker FASTA was written to GCF_025821785.1_ASM2582178v1_genomic.fna/markers.fasta
[2024-01-24 11:21:11,364] [INFO] Task started: Blastn
[2024-01-24 11:21:11,364] [INFO] Running command: blastn -query GCF_025821785.1_ASM2582178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga68d7a7e-c376-4d8c-8e80-aefa0394763e/dqc_reference/reference_markers.fasta -out GCF_025821785.1_ASM2582178v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:12,528] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:12,537] [INFO] Selected 13 target genomes.
[2024-01-24 11:21:12,538] [INFO] Target genome list was writen to GCF_025821785.1_ASM2582178v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:12,543] [INFO] Task started: fastANI
[2024-01-24 11:21:12,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg679b91f7-5715-4c29-84e8-1f78bdf0e328/GCF_025821785.1_ASM2582178v1_genomic.fna.gz --refList GCF_025821785.1_ASM2582178v1_genomic.fna/target_genomes.txt --output GCF_025821785.1_ASM2582178v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:30,985] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:30,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga68d7a7e-c376-4d8c-8e80-aefa0394763e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:30,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga68d7a7e-c376-4d8c-8e80-aefa0394763e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:30,999] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:30,999] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:30,999] [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
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	99.998	2025	2025	95	conclusive
Mycobacterium florentinum	strain=DSM 44852	GCA_002101635.1	292462	292462	type	True	90.36	1682	2025	95	below_threshold
Mycobacterium florentinum	strain=JCM 14740	GCA_010730355.1	292462	292462	type	True	90.3292	1701	2025	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_002102415.1	47839	47839	type	True	88.1685	1594	2025	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_000689255.1	47839	47839	type	True	88.13	1584	2025	95	below_threshold
Mycobacterium lentiflavum	strain=ATCC 51985	GCA_022374895.2	141349	141349	type	True	87.4991	1584	2025	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	87.3677	1613	2025	95	below_threshold
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	87.0991	1388	2025	95	below_threshold
Mycobacterium simiae	strain=JCM 12377	GCA_010727605.1	1784	1784	type	True	83.1938	1399	2025	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	82.8731	1316	2025	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	82.2893	1197	2025	95	below_threshold
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	82.265	1222	2025	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	82.1563	1219	2025	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:31,001] [INFO] DFAST Taxonomy check result was written to GCF_025821785.1_ASM2582178v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:31,001] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:31,002] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:31,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga68d7a7e-c376-4d8c-8e80-aefa0394763e/dqc_reference/checkm_data
[2024-01-24 11:21:31,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:31,062] [INFO] Task started: CheckM
[2024-01-24 11:21:31,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821785.1_ASM2582178v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821785.1_ASM2582178v1_genomic.fna/checkm_input GCF_025821785.1_ASM2582178v1_genomic.fna/checkm_result
[2024-01-24 11:22:26,719] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:26,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:26,740] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:26,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:26,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821785.1_ASM2582178v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:26,741] [INFO] Task started: Blastn
[2024-01-24 11:22:26,742] [INFO] Running command: blastn -query GCF_025821785.1_ASM2582178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga68d7a7e-c376-4d8c-8e80-aefa0394763e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821785.1_ASM2582178v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:28,362] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:28,366] [INFO] Selected 14 target genomes.
[2024-01-24 11:22:28,366] [INFO] Target genome list was writen to GCF_025821785.1_ASM2582178v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:28,381] [INFO] Task started: fastANI
[2024-01-24 11:22:28,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg679b91f7-5715-4c29-84e8-1f78bdf0e328/GCF_025821785.1_ASM2582178v1_genomic.fna.gz --refList GCF_025821785.1_ASM2582178v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821785.1_ASM2582178v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:48,691] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:48,708] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:48,708] [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_010731715.1	s__Mycobacterium stomatepiae	99.998	2025	2025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010730355.1	s__Mycobacterium florentinum	90.3292	1701	2025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000689255.1	s__Mycobacterium triplex	88.1214	1585	2025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001373395.1	s__Mycobacterium lentiflavum	87.5152	1600	2025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176255.2	s__Mycobacterium ahvazicum	87.367	1612	2025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526915.1	s__Mycobacterium genavense	87.0991	1388	2025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112775.1	s__Mycobacterium montefiorense	86.0791	1552	2025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727605.1	s__Mycobacterium simiae	83.1933	1398	2025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	97.21	0.97	0.92	4	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	82.8615	1319	2025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673535.1	s__Mycobacterium sp001673535	82.5532	1223	2025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672915.1	s__Mycobacterium sp001672915	82.4902	1231	2025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672755.1	s__Mycobacterium colombiense_C	82.3495	1188	2025	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672815.1	s__Mycobacterium sp001672815	82.3476	1211	2025	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	81.986	1162	2025	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 11:22:48,710] [INFO] GTDB search result was written to GCF_025821785.1_ASM2582178v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:48,711] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:48,714] [INFO] DFAST_QC result json was written to GCF_025821785.1_ASM2582178v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:48,715] [INFO] DFAST_QC completed!
[2024-01-24 11:22:48,715] [INFO] Total running time: 0h1m59s