[2024-01-24 13:22:14,005] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:14,008] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:14,008] [INFO] DQC Reference Directory: /var/lib/cwl/stgb35d8a58-39c6-44b1-8b3d-5630133c5b9c/dqc_reference
[2024-01-24 13:22:15,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:15,240] [INFO] Task started: Prodigal
[2024-01-24 13:22:15,241] [INFO] Running command: gunzip -c /var/lib/cwl/stga86907a8-3a9f-4794-b10c-ceac360d4cbd/GCF_025823305.1_ASM2582330v1_genomic.fna.gz | prodigal -d GCF_025823305.1_ASM2582330v1_genomic.fna/cds.fna -a GCF_025823305.1_ASM2582330v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:39,420] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:39,421] [INFO] Task started: HMMsearch
[2024-01-24 13:22:39,421] [INFO] Running command: hmmsearch --tblout GCF_025823305.1_ASM2582330v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb35d8a58-39c6-44b1-8b3d-5630133c5b9c/dqc_reference/reference_markers.hmm GCF_025823305.1_ASM2582330v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:39,934] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:39,935] [INFO] Found 6/6 markers.
[2024-01-24 13:22:39,989] [INFO] Query marker FASTA was written to GCF_025823305.1_ASM2582330v1_genomic.fna/markers.fasta
[2024-01-24 13:22:39,989] [INFO] Task started: Blastn
[2024-01-24 13:22:39,990] [INFO] Running command: blastn -query GCF_025823305.1_ASM2582330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb35d8a58-39c6-44b1-8b3d-5630133c5b9c/dqc_reference/reference_markers.fasta -out GCF_025823305.1_ASM2582330v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:41,371] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:41,375] [INFO] Selected 9 target genomes.
[2024-01-24 13:22:41,375] [INFO] Target genome list was writen to GCF_025823305.1_ASM2582330v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:41,377] [INFO] Task started: fastANI
[2024-01-24 13:22:41,377] [INFO] Running command: fastANI --query /var/lib/cwl/stga86907a8-3a9f-4794-b10c-ceac360d4cbd/GCF_025823305.1_ASM2582330v1_genomic.fna.gz --refList GCF_025823305.1_ASM2582330v1_genomic.fna/target_genomes.txt --output GCF_025823305.1_ASM2582330v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:56,598] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:56,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb35d8a58-39c6-44b1-8b3d-5630133c5b9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:56,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb35d8a58-39c6-44b1-8b3d-5630133c5b9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:56,614] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:56,614] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:56,614] [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 florentinum	strain=JCM 14740	GCA_010730355.1	292462	292462	type	True	99.9967	2056	2056	95	conclusive
Mycobacterium florentinum	strain=DSM 44852	GCA_002101635.1	292462	292462	type	True	99.9924	2035	2056	95	conclusive
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	90.3466	1702	2056	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_002102415.1	47839	47839	type	True	89.4734	1751	2056	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_000689255.1	47839	47839	type	True	89.4319	1773	2056	95	below_threshold
Mycobacterium lentiflavum	strain=ATCC 51985	GCA_022374895.2	141349	141349	type	True	88.5937	1583	2056	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	88.3291	1579	2056	95	below_threshold
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	88.2485	1399	2056	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	83.3445	1373	2056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:56,616] [INFO] DFAST Taxonomy check result was written to GCF_025823305.1_ASM2582330v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:56,617] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:56,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:56,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb35d8a58-39c6-44b1-8b3d-5630133c5b9c/dqc_reference/checkm_data
[2024-01-24 13:22:56,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:56,678] [INFO] Task started: CheckM
[2024-01-24 13:22:56,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025823305.1_ASM2582330v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025823305.1_ASM2582330v1_genomic.fna/checkm_input GCF_025823305.1_ASM2582330v1_genomic.fna/checkm_result
[2024-01-24 13:24:05,983] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:05,984] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:06,022] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:06,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:06,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025823305.1_ASM2582330v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:06,024] [INFO] Task started: Blastn
[2024-01-24 13:24:06,025] [INFO] Running command: blastn -query GCF_025823305.1_ASM2582330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb35d8a58-39c6-44b1-8b3d-5630133c5b9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_025823305.1_ASM2582330v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:07,853] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:07,857] [INFO] Selected 11 target genomes.
[2024-01-24 13:24:07,857] [INFO] Target genome list was writen to GCF_025823305.1_ASM2582330v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:07,861] [INFO] Task started: fastANI
[2024-01-24 13:24:07,861] [INFO] Running command: fastANI --query /var/lib/cwl/stga86907a8-3a9f-4794-b10c-ceac360d4cbd/GCF_025823305.1_ASM2582330v1_genomic.fna.gz --refList GCF_025823305.1_ASM2582330v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025823305.1_ASM2582330v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:23,976] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:23,992] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:23,993] [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_010730355.1	s__Mycobacterium florentinum	99.9967	2056	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_010731715.1	s__Mycobacterium stomatepiae	90.3509	1701	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000689255.1	s__Mycobacterium triplex	89.4304	1772	2056	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	88.637	1667	2056	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	88.3243	1578	2056	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	88.2408	1401	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665235.1	s__Mycobacterium sp001665235	85.1158	1493	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	83.3249	1377	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667275.1	s__Mycobacterium sp001667275	82.6794	1253	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_002102155.1	s__Mycobacterium europaeum	82.6669	1203	2056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_001907675.1	s__Mycobacterium paraffinicum	82.4006	1237	2056	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 13:24:23,994] [INFO] GTDB search result was written to GCF_025823305.1_ASM2582330v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:23,995] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:23,998] [INFO] DFAST_QC result json was written to GCF_025823305.1_ASM2582330v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:23,999] [INFO] DFAST_QC completed!
[2024-01-24 13:24:23,999] [INFO] Total running time: 0h2m10s