[2024-01-25 18:40:50,630] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:50,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:50,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg518fc9c9-e5c6-4c15-9524-9343d9c91d26/dqc_reference
[2024-01-25 18:40:51,763] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:51,764] [INFO] Task started: Prodigal
[2024-01-25 18:40:51,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg752d8dee-bf51-46fc-ba1a-24cd66fd3cbc/GCF_002086335.1_ASM208633v1_genomic.fna.gz | prodigal -d GCF_002086335.1_ASM208633v1_genomic.fna/cds.fna -a GCF_002086335.1_ASM208633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:12,012] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:12,012] [INFO] Task started: HMMsearch
[2024-01-25 18:41:12,012] [INFO] Running command: hmmsearch --tblout GCF_002086335.1_ASM208633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg518fc9c9-e5c6-4c15-9524-9343d9c91d26/dqc_reference/reference_markers.hmm GCF_002086335.1_ASM208633v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:12,284] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:12,286] [INFO] Found 6/6 markers.
[2024-01-25 18:41:12,336] [INFO] Query marker FASTA was written to GCF_002086335.1_ASM208633v1_genomic.fna/markers.fasta
[2024-01-25 18:41:12,336] [INFO] Task started: Blastn
[2024-01-25 18:41:12,336] [INFO] Running command: blastn -query GCF_002086335.1_ASM208633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg518fc9c9-e5c6-4c15-9524-9343d9c91d26/dqc_reference/reference_markers.fasta -out GCF_002086335.1_ASM208633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:13,491] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:13,495] [INFO] Selected 10 target genomes.
[2024-01-25 18:41:13,496] [INFO] Target genome list was writen to GCF_002086335.1_ASM208633v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:13,500] [INFO] Task started: fastANI
[2024-01-25 18:41:13,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg752d8dee-bf51-46fc-ba1a-24cd66fd3cbc/GCF_002086335.1_ASM208633v1_genomic.fna.gz --refList GCF_002086335.1_ASM208633v1_genomic.fna/target_genomes.txt --output GCF_002086335.1_ASM208633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:28,392] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:28,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg518fc9c9-e5c6-4c15-9524-9343d9c91d26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:28,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg518fc9c9-e5c6-4c15-9524-9343d9c91d26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:28,400] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:41:28,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:28,400] [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 mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	100.0	1984	1986	95	conclusive
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	99.9968	1985	1986	95	conclusive
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	89.4024	1524	1986	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	89.382	1529	1986	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	88.2931	1396	1986	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	86.9819	1487	1986	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	86.9757	1485	1986	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	86.8523	1497	1986	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	86.8155	1440	1986	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	86.7239	1426	1986	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:28,402] [INFO] DFAST Taxonomy check result was written to GCF_002086335.1_ASM208633v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:28,402] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:28,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:28,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg518fc9c9-e5c6-4c15-9524-9343d9c91d26/dqc_reference/checkm_data
[2024-01-25 18:41:28,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:28,459] [INFO] Task started: CheckM
[2024-01-25 18:41:28,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086335.1_ASM208633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086335.1_ASM208633v1_genomic.fna/checkm_input GCF_002086335.1_ASM208633v1_genomic.fna/checkm_result
[2024-01-25 18:42:27,405] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:27,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:27,430] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:27,430] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:27,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086335.1_ASM208633v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:27,431] [INFO] Task started: Blastn
[2024-01-25 18:42:27,431] [INFO] Running command: blastn -query GCF_002086335.1_ASM208633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg518fc9c9-e5c6-4c15-9524-9343d9c91d26/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086335.1_ASM208633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:29,111] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:29,114] [INFO] Selected 14 target genomes.
[2024-01-25 18:42:29,114] [INFO] Target genome list was writen to GCF_002086335.1_ASM208633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:29,122] [INFO] Task started: fastANI
[2024-01-25 18:42:29,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg752d8dee-bf51-46fc-ba1a-24cd66fd3cbc/GCF_002086335.1_ASM208633v1_genomic.fna.gz --refList GCF_002086335.1_ASM208633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086335.1_ASM208633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:49,832] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:49,840] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:49,841] [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_010731775.1	s__Mycobacterium mantenii	99.9968	1985	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.19	95.22	0.92	0.90	6	conclusive
GCF_001665835.1	s__Mycobacterium colombiense_A	89.9556	1501	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953985.1	s__Mycobacterium colombiense_B	89.7988	1539	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
GCF_001672755.1	s__Mycobacterium colombiense_C	89.7101	1509	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104765.1	s__Mycobacterium vulneris	89.66	1601	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665875.1	s__Mycobacterium sp001665875	89.657	1468	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	89.4024	1524	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_003284975.1	s__Mycobacterium europaeum_A	88.735	1392	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.84	95.70	0.84	0.79	6	-
GCF_001667145.1	s__Mycobacterium sp001667145	88.5464	1409	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086125.1	s__Mycobacterium arosiense	88.2931	1396	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672975.1	s__Mycobacterium sp001672975	88.0662	1407	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667315.1	s__Mycobacterium sp001667315	87.0634	1397	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731675.1	s__Mycobacterium marseillense	86.8175	1439	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	-
GCF_002102255.1	s__Mycobacterium nebraskense	84.4853	1413	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:49,842] [INFO] GTDB search result was written to GCF_002086335.1_ASM208633v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:49,842] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:49,846] [INFO] DFAST_QC result json was written to GCF_002086335.1_ASM208633v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:49,846] [INFO] DFAST_QC completed!
[2024-01-25 18:42:49,846] [INFO] Total running time: 0h1m59s