[2024-01-25 19:03:20,579] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:20,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:20,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg76dbe140-e986-4f56-9b0c-e706737380c3/dqc_reference
[2024-01-25 19:03:21,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:21,735] [INFO] Task started: Prodigal
[2024-01-25 19:03:21,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg68339ce3-b301-4a34-b8ad-c4ef27449b28/GCF_002013895.1_ASM201389v1_genomic.fna.gz | prodigal -d GCF_002013895.1_ASM201389v1_genomic.fna/cds.fna -a GCF_002013895.1_ASM201389v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:38,125] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:38,125] [INFO] Task started: HMMsearch
[2024-01-25 19:03:38,125] [INFO] Running command: hmmsearch --tblout GCF_002013895.1_ASM201389v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76dbe140-e986-4f56-9b0c-e706737380c3/dqc_reference/reference_markers.hmm GCF_002013895.1_ASM201389v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:38,400] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:38,401] [INFO] Found 6/6 markers.
[2024-01-25 19:03:38,445] [INFO] Query marker FASTA was written to GCF_002013895.1_ASM201389v1_genomic.fna/markers.fasta
[2024-01-25 19:03:38,445] [INFO] Task started: Blastn
[2024-01-25 19:03:38,445] [INFO] Running command: blastn -query GCF_002013895.1_ASM201389v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76dbe140-e986-4f56-9b0c-e706737380c3/dqc_reference/reference_markers.fasta -out GCF_002013895.1_ASM201389v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:39,454] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:39,457] [INFO] Selected 15 target genomes.
[2024-01-25 19:03:39,457] [INFO] Target genome list was writen to GCF_002013895.1_ASM201389v1_genomic.fna/target_genomes.txt
[2024-01-25 19:03:39,468] [INFO] Task started: fastANI
[2024-01-25 19:03:39,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg68339ce3-b301-4a34-b8ad-c4ef27449b28/GCF_002013895.1_ASM201389v1_genomic.fna.gz --refList GCF_002013895.1_ASM201389v1_genomic.fna/target_genomes.txt --output GCF_002013895.1_ASM201389v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:57,468] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:57,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76dbe140-e986-4f56-9b0c-e706737380c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:57,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76dbe140-e986-4f56-9b0c-e706737380c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:57,479] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:03:57,479] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:03:57,479] [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=CV002	GCA_002013895.1	948102	948102	type	True	100.0	1790	1795	95	conclusive
Mycobacteroides franklinii	strain=DSM 45524	GCA_004355025.1	948102	948102	type	True	99.9979	1779	1795	95	conclusive
Mycobacteroides franklinii	strain=DSM 45524	GCA_002086225.1	948102	948102	type	True	99.9874	1777	1795	95	conclusive
Mycobacteroides immunogenum	strain=CCUG 47286	GCA_001605725.1	83262	83262	type	True	86.5774	1427	1795	95	below_threshold
Mycobacteroides immunogenum	strain=MC 779	GCA_002013555.1	83262	83262	type	True	86.574	1412	1795	95	below_threshold
Mycobacteroides abscessus subsp. bolletii	strain=CCUG 50184	GCA_006409125.1	319705	36809	type	True	85.9299	1344	1795	95	below_threshold
Mycobacteroides abscessus	strain=ATCC 19977	GCA_000069185.1	36809	36809	type	True	85.8781	1324	1795	95	below_threshold
Mycobacteroides abscessus subsp. bolletii	strain=BD	GCA_000239035.2	319705	36809	type	True	85.8633	1367	1795	95	below_threshold
Mycobacteroides abscessus	strain=NCTC13031	GCA_900453225.1	36809	36809	type	True	85.8496	1331	1795	95	below_threshold
Mycobacteroides abscessus subsp. massiliense	strain=CCUG 48898	GCA_000239055.2	1962118	36809	type	True	85.8302	1366	1795	95	below_threshold
Mycobacteroides abscessus subsp. massiliense	strain=JCM 15300	GCA_000497265.2	1962118	36809	type	True	85.7487	1380	1795	95	below_threshold
Mycobacteroides salmoniphilum	strain=SC	GCA_002013685.1	404941	404941	suspected-type	True	85.6107	1286	1795	95	below_threshold
Mycobacteroides salmoniphilum	strain=DSM 43276	GCA_004924335.1	404941	404941	suspected-type	True	85.5143	1334	1795	95	below_threshold
[Mycobacterium] stephanolepidis	strain=NJB0901	GCA_002356335.1	1520670	1520670	type	True	85.2019	1302	1795	95	below_threshold
Mycobacteroides chelonae	strain=CCUG 47445	GCA_001632805.1	1774	1774	suspected-type	True	85.0785	1302	1795	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:57,480] [INFO] DFAST Taxonomy check result was written to GCF_002013895.1_ASM201389v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:57,481] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:57,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:57,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76dbe140-e986-4f56-9b0c-e706737380c3/dqc_reference/checkm_data
[2024-01-25 19:03:57,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:57,533] [INFO] Task started: CheckM
[2024-01-25 19:03:57,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002013895.1_ASM201389v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002013895.1_ASM201389v1_genomic.fna/checkm_input GCF_002013895.1_ASM201389v1_genomic.fna/checkm_result
[2024-01-25 19:04:45,758] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:45,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:45,778] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:45,778] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:45,779] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002013895.1_ASM201389v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:45,779] [INFO] Task started: Blastn
[2024-01-25 19:04:45,779] [INFO] Running command: blastn -query GCF_002013895.1_ASM201389v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76dbe140-e986-4f56-9b0c-e706737380c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002013895.1_ASM201389v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:47,248] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:47,250] [INFO] Selected 12 target genomes.
[2024-01-25 19:04:47,250] [INFO] Target genome list was writen to GCF_002013895.1_ASM201389v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:47,254] [INFO] Task started: fastANI
[2024-01-25 19:04:47,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg68339ce3-b301-4a34-b8ad-c4ef27449b28/GCF_002013895.1_ASM201389v1_genomic.fna.gz --refList GCF_002013895.1_ASM201389v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002013895.1_ASM201389v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:01,674] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:01,683] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:01,683] [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	100.0	1790	1795	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	86.5773	1427	1795	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	85.865	1326	1795	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	85.76	1330	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.45	98.92	0.97	0.95	3	-
GCF_001456355.1	s__Mycobacterium saopaulense	85.7596	1333	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.82	98.51	0.95	0.95	4	-
GCF_002013415.1	s__Mycobacterium sp002013415	85.7263	1333	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.14	98.85	0.92	0.91	4	-
GCF_002013465.1	s__Mycobacterium sp002013465	85.6231	1319	1795	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	85.4996	1336	1795	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	85.2608	1107	1795	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	85.2071	1301	1795	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	85.0851	1301	1795	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	84.1936	1293	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:01,684] [INFO] GTDB search result was written to GCF_002013895.1_ASM201389v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:01,685] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:01,688] [INFO] DFAST_QC result json was written to GCF_002013895.1_ASM201389v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:01,688] [INFO] DFAST_QC completed!
[2024-01-25 19:05:01,688] [INFO] Total running time: 0h1m41s