[2024-01-24 11:18:17,702] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:18:17,704] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:18:17,704] [INFO] DQC Reference Directory: /var/lib/cwl/stgc12f629f-8674-4476-8e3f-e6b058ab46d2/dqc_reference
[2024-01-24 11:18:19,086] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:18:19,087] [INFO] Task started: Prodigal
[2024-01-24 11:18:19,087] [INFO] Running command: gunzip -c /var/lib/cwl/stg7359555d-b2db-464f-a800-92ca6a11e90b/GCF_002086735.1_ASM208673v1_genomic.fna.gz | prodigal -d GCF_002086735.1_ASM208673v1_genomic.fna/cds.fna -a GCF_002086735.1_ASM208673v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:18:37,917] [INFO] Task succeeded: Prodigal
[2024-01-24 11:18:37,918] [INFO] Task started: HMMsearch
[2024-01-24 11:18:37,918] [INFO] Running command: hmmsearch --tblout GCF_002086735.1_ASM208673v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc12f629f-8674-4476-8e3f-e6b058ab46d2/dqc_reference/reference_markers.hmm GCF_002086735.1_ASM208673v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:18:38,214] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:18:38,216] [INFO] Found 6/6 markers.
[2024-01-24 11:18:38,266] [INFO] Query marker FASTA was written to GCF_002086735.1_ASM208673v1_genomic.fna/markers.fasta
[2024-01-24 11:18:38,266] [INFO] Task started: Blastn
[2024-01-24 11:18:38,266] [INFO] Running command: blastn -query GCF_002086735.1_ASM208673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc12f629f-8674-4476-8e3f-e6b058ab46d2/dqc_reference/reference_markers.fasta -out GCF_002086735.1_ASM208673v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:39,405] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:39,409] [INFO] Selected 13 target genomes.
[2024-01-24 11:18:39,409] [INFO] Target genome list was writen to GCF_002086735.1_ASM208673v1_genomic.fna/target_genomes.txt
[2024-01-24 11:18:39,418] [INFO] Task started: fastANI
[2024-01-24 11:18:39,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg7359555d-b2db-464f-a800-92ca6a11e90b/GCF_002086735.1_ASM208673v1_genomic.fna.gz --refList GCF_002086735.1_ASM208673v1_genomic.fna/target_genomes.txt --output GCF_002086735.1_ASM208673v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:18:57,385] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:57,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc12f629f-8674-4476-8e3f-e6b058ab46d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:18:57,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc12f629f-8674-4476-8e3f-e6b058ab46d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:18:57,397] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:18:57,397] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:18:57,398] [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 nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	90.1526	1643	1979	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	88.5428	1491	1979	95	below_threshold
Mycobacterium paraseoulense	strain=JCM 16952	GCA_010731655.1	590652	590652	type	True	88.3658	1529	1979	95	below_threshold
Mycobacterium paraseoulense	strain=DSM 45000	GCA_002086475.1	590652	590652	type	True	88.3547	1495	1979	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	85.1191	1389	1979	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	85.1171	1389	1979	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	84.3498	1358	1979	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	84.3423	1383	1979	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	84.3352	1357	1979	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	84.3239	1344	1979	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	84.2781	1418	1979	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	84.2536	1340	1979	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	83.5065	1262	1979	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:18:57,399] [INFO] DFAST Taxonomy check result was written to GCF_002086735.1_ASM208673v1_genomic.fna/tc_result.tsv
[2024-01-24 11:18:57,399] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:18:57,400] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:18:57,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc12f629f-8674-4476-8e3f-e6b058ab46d2/dqc_reference/checkm_data
[2024-01-24 11:18:57,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:18:57,456] [INFO] Task started: CheckM
[2024-01-24 11:18:57,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086735.1_ASM208673v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086735.1_ASM208673v1_genomic.fna/checkm_input GCF_002086735.1_ASM208673v1_genomic.fna/checkm_result
[2024-01-24 11:19:53,150] [INFO] Task succeeded: CheckM
[2024-01-24 11:19:53,151] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:19:53,179] [INFO] ===== Completeness check finished =====
[2024-01-24 11:19:53,179] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:19:53,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086735.1_ASM208673v1_genomic.fna/markers.fasta)
[2024-01-24 11:19:53,180] [INFO] Task started: Blastn
[2024-01-24 11:19:53,180] [INFO] Running command: blastn -query GCF_002086735.1_ASM208673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc12f629f-8674-4476-8e3f-e6b058ab46d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086735.1_ASM208673v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:19:54,789] [INFO] Task succeeded: Blastn
[2024-01-24 11:19:54,793] [INFO] Selected 12 target genomes.
[2024-01-24 11:19:54,794] [INFO] Target genome list was writen to GCF_002086735.1_ASM208673v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:19:54,828] [INFO] Task started: fastANI
[2024-01-24 11:19:54,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg7359555d-b2db-464f-a800-92ca6a11e90b/GCF_002086735.1_ASM208673v1_genomic.fna.gz --refList GCF_002086735.1_ASM208673v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086735.1_ASM208673v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:20:12,461] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:12,475] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:20:12,475] [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_002086735.1	s__Mycobacterium scrofulaceum	100.0	1971	1979	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_000164135.1	s__Mycobacterium parascrofulaceum	94.23	1700	1979	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_002102255.1	s__Mycobacterium nebraskense	90.1431	1644	1979	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
GCF_001665605.1	s__Mycobacterium sp001665605	88.613	1487	1979	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.77	98.77	0.96	0.96	2	-
GCF_010731595.1	s__Mycobacterium seoulense	88.559	1489	1979	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667075.1	s__Mycobacterium sp001667075	88.4342	1483	1979	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.38	0.97	0.97	3	-
GCF_002102155.1	s__Mycobacterium europaeum	88.4162	1551	1979	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_900240975.1	s__Mycobacterium sp900240975	88.4012	1509	1979	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_010731655.1	s__Mycobacterium paraseoulense	88.349	1531	1979	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001667735.1	s__Mycobacterium sp001667735	87.9995	1457	1979	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.16	0.95	0.92	6	-
GCF_001667275.1	s__Mycobacterium sp001667275	87.9891	1445	1979	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_010731775.1	s__Mycobacterium mantenii	84.2523	1422	1979	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.19	95.22	0.92	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:20:12,477] [INFO] GTDB search result was written to GCF_002086735.1_ASM208673v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:20:12,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:20:12,481] [INFO] DFAST_QC result json was written to GCF_002086735.1_ASM208673v1_genomic.fna/dqc_result.json
[2024-01-24 11:20:12,481] [INFO] DFAST_QC completed!
[2024-01-24 11:20:12,481] [INFO] Total running time: 0h1m55s