[2024-01-24 14:55:50,971] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:50,975] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:50,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b359c5f-cd1a-4519-8b00-1d90139f8df7/dqc_reference
[2024-01-24 14:55:52,266] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:52,267] [INFO] Task started: Prodigal
[2024-01-24 14:55:52,267] [INFO] Running command: gunzip -c /var/lib/cwl/stgd49e1e0c-00f8-4aae-b2e9-9447bdea2d60/GCF_004355025.1_ASM435502v1_genomic.fna.gz | prodigal -d GCF_004355025.1_ASM435502v1_genomic.fna/cds.fna -a GCF_004355025.1_ASM435502v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:13,024] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:13,024] [INFO] Task started: HMMsearch
[2024-01-24 14:56:13,024] [INFO] Running command: hmmsearch --tblout GCF_004355025.1_ASM435502v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b359c5f-cd1a-4519-8b00-1d90139f8df7/dqc_reference/reference_markers.hmm GCF_004355025.1_ASM435502v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:13,333] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:13,335] [INFO] Found 6/6 markers.
[2024-01-24 14:56:13,380] [INFO] Query marker FASTA was written to GCF_004355025.1_ASM435502v1_genomic.fna/markers.fasta
[2024-01-24 14:56:13,381] [INFO] Task started: Blastn
[2024-01-24 14:56:13,381] [INFO] Running command: blastn -query GCF_004355025.1_ASM435502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b359c5f-cd1a-4519-8b00-1d90139f8df7/dqc_reference/reference_markers.fasta -out GCF_004355025.1_ASM435502v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:14,448] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:14,450] [INFO] Selected 15 target genomes.
[2024-01-24 14:56:14,451] [INFO] Target genome list was writen to GCF_004355025.1_ASM435502v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:14,457] [INFO] Task started: fastANI
[2024-01-24 14:56:14,457] [INFO] Running command: fastANI --query /var/lib/cwl/stgd49e1e0c-00f8-4aae-b2e9-9447bdea2d60/GCF_004355025.1_ASM435502v1_genomic.fna.gz --refList GCF_004355025.1_ASM435502v1_genomic.fna/target_genomes.txt --output GCF_004355025.1_ASM435502v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:32,368] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:32,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b359c5f-cd1a-4519-8b00-1d90139f8df7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:32,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b359c5f-cd1a-4519-8b00-1d90139f8df7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:32,382] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:56:32,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:32,383] [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 franklinii	strain=DSM 45524	GCA_004355025.1	948102	948102	type	True	100.0	1786	1790	95	conclusive
Mycobacteroides franklinii	strain=CV002	GCA_002013895.1	948102	948102	type	True	99.9901	1777	1790	95	conclusive
Mycobacteroides franklinii	strain=DSM 45524	GCA_002086225.1	948102	948102	type	True	99.9804	1757	1790	95	conclusive
Mycobacteroides immunogenum	strain=MC 779	GCA_002013555.1	83262	83262	type	True	86.5838	1418	1790	95	below_threshold
Mycobacteroides immunogenum	strain=CCUG 47286	GCA_001605725.1	83262	83262	type	True	86.5682	1429	1790	95	below_threshold
Mycobacteroides abscessus subsp. bolletii	strain=BD	GCA_000239035.2	319705	36809	type	True	85.8853	1362	1790	95	below_threshold
Mycobacteroides abscessus subsp. bolletii	strain=CCUG 50184	GCA_006409125.1	319705	36809	type	True	85.8585	1352	1790	95	below_threshold
Mycobacteroides abscessus	strain=NCTC13031	GCA_900453225.1	36809	36809	type	True	85.8429	1349	1790	95	below_threshold
Mycobacteroides abscessus subsp. massiliense	strain=CCUG 48898	GCA_000239055.2	1962118	36809	type	True	85.8424	1346	1790	95	below_threshold
Mycobacteroides abscessus	strain=ATCC 19977	GCA_000069185.1	36809	36809	type	True	85.8365	1348	1790	95	below_threshold
Mycobacteroides abscessus subsp. massiliense	strain=JCM 15300	GCA_000497265.2	1962118	36809	type	True	85.8315	1381	1790	95	below_threshold
Mycobacteroides salmoniphilum	strain=SC	GCA_002013685.1	404941	404941	suspected-type	True	85.5614	1296	1790	95	below_threshold
Mycobacteroides salmoniphilum	strain=DSM 43276	GCA_004924335.1	404941	404941	suspected-type	True	85.5441	1318	1790	95	below_threshold
[Mycobacterium] stephanolepidis	strain=NJB0901	GCA_002356335.1	1520670	1520670	type	True	85.1863	1297	1790	95	below_threshold
Mycobacteroides chelonae	strain=CCUG 47445	GCA_001632805.1	1774	1774	suspected-type	True	85.0637	1306	1790	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:32,385] [INFO] DFAST Taxonomy check result was written to GCF_004355025.1_ASM435502v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:32,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:32,386] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:32,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b359c5f-cd1a-4519-8b00-1d90139f8df7/dqc_reference/checkm_data
[2024-01-24 14:56:32,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:32,438] [INFO] Task started: CheckM
[2024-01-24 14:56:32,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004355025.1_ASM435502v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004355025.1_ASM435502v1_genomic.fna/checkm_input GCF_004355025.1_ASM435502v1_genomic.fna/checkm_result
[2024-01-24 14:57:31,704] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:31,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:31,735] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:31,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:31,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004355025.1_ASM435502v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:31,737] [INFO] Task started: Blastn
[2024-01-24 14:57:31,737] [INFO] Running command: blastn -query GCF_004355025.1_ASM435502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b359c5f-cd1a-4519-8b00-1d90139f8df7/dqc_reference/reference_markers_gtdb.fasta -out GCF_004355025.1_ASM435502v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:33,267] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:33,271] [INFO] Selected 12 target genomes.
[2024-01-24 14:57:33,271] [INFO] Target genome list was writen to GCF_004355025.1_ASM435502v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:33,281] [INFO] Task started: fastANI
[2024-01-24 14:57:33,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgd49e1e0c-00f8-4aae-b2e9-9447bdea2d60/GCF_004355025.1_ASM435502v1_genomic.fna.gz --refList GCF_004355025.1_ASM435502v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004355025.1_ASM435502v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:47,617] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:47,634] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:47,634] [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_002013895.1	s__Mycobacterium franklinii	99.9901	1777	1790	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.20	95.66	0.94	0.87	12	conclusive
GCF_001605725.1	s__Mycobacterium immunogenum	86.5726	1428	1790	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.78	96.59	0.98	0.90	18	-
GCA_000069185.1	s__Mycobacterium abscessus	85.8367	1348	1790	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	96.83	0.93	0.86	1820	-
GCF_002013375.1	s__Mycobacterium sp002013375	85.7295	1351	1790	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.45	98.92	0.97	0.95	3	-
GCF_002013415.1	s__Mycobacterium sp002013415	85.6882	1342	1790	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.14	98.85	0.92	0.91	4	-
GCF_001456355.1	s__Mycobacterium saopaulense	85.6833	1338	1790	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.82	98.51	0.95	0.95	4	-
GCF_002013465.1	s__Mycobacterium sp002013465	85.6377	1312	1790	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.45	95.17	0.93	0.91	7	-
GCF_004924335.1	s__Mycobacterium salmoniphilum	85.5405	1318	1790	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.49	96.58	0.95	0.92	5	-
GCF_014204435.1	s__Mycobacterium chelonae_A	85.2627	1100	1790	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	85.1839	1298	1790	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632805.1	s__Mycobacterium chelonae	85.0765	1306	1790	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.73	95.27	0.90	0.84	73	-
GCF_013449725.1	s__Mycobacterium sp013449725	84.2287	1292	1790	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 14:57:47,636] [INFO] GTDB search result was written to GCF_004355025.1_ASM435502v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:47,637] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:47,641] [INFO] DFAST_QC result json was written to GCF_004355025.1_ASM435502v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:47,642] [INFO] DFAST_QC completed!
[2024-01-24 14:57:47,642] [INFO] Total running time: 0h1m57s