[2024-01-24 14:38:48,683] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:48,690] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:48,691] [INFO] DQC Reference Directory: /var/lib/cwl/stg90e13bf0-d49a-400b-a7e8-1b75751719e4/dqc_reference
[2024-01-24 14:38:50,448] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:50,449] [INFO] Task started: Prodigal
[2024-01-24 14:38:50,449] [INFO] Running command: gunzip -c /var/lib/cwl/stg08dbd542-293b-4e2e-9299-329de02b871c/GCF_004924335.1_ASM492433v1_genomic.fna.gz | prodigal -d GCF_004924335.1_ASM492433v1_genomic.fna/cds.fna -a GCF_004924335.1_ASM492433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:17,892] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:17,893] [INFO] Task started: HMMsearch
[2024-01-24 14:39:17,893] [INFO] Running command: hmmsearch --tblout GCF_004924335.1_ASM492433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90e13bf0-d49a-400b-a7e8-1b75751719e4/dqc_reference/reference_markers.hmm GCF_004924335.1_ASM492433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:18,279] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:18,280] [INFO] Found 6/6 markers.
[2024-01-24 14:39:18,325] [INFO] Query marker FASTA was written to GCF_004924335.1_ASM492433v1_genomic.fna/markers.fasta
[2024-01-24 14:39:18,325] [INFO] Task started: Blastn
[2024-01-24 14:39:18,325] [INFO] Running command: blastn -query GCF_004924335.1_ASM492433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90e13bf0-d49a-400b-a7e8-1b75751719e4/dqc_reference/reference_markers.fasta -out GCF_004924335.1_ASM492433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:19,462] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:19,466] [INFO] Selected 10 target genomes.
[2024-01-24 14:39:19,466] [INFO] Target genome list was writen to GCF_004924335.1_ASM492433v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:19,470] [INFO] Task started: fastANI
[2024-01-24 14:39:19,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg08dbd542-293b-4e2e-9299-329de02b871c/GCF_004924335.1_ASM492433v1_genomic.fna.gz --refList GCF_004924335.1_ASM492433v1_genomic.fna/target_genomes.txt --output GCF_004924335.1_ASM492433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:32,678] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:32,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90e13bf0-d49a-400b-a7e8-1b75751719e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:32,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90e13bf0-d49a-400b-a7e8-1b75751719e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:32,689] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:32,689] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:32,689] [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 salmoniphilum	strain=DSM 43276	GCA_004924335.1	404941	404941	suspected-type	True	100.0	1592	1592	95	conclusive
Mycobacteroides salmoniphilum	strain=SC	GCA_002013685.1	404941	404941	suspected-type	True	99.9604	1553	1592	95	conclusive
[Mycobacterium] stephanolepidis	strain=NJB0901	GCA_002356335.1	1520670	1520670	type	True	87.8585	1373	1592	95	below_threshold
Mycobacteroides chelonae	strain=ATCC 35752	GCA_000971805.1	1774	1774	suspected-type	True	87.4841	1352	1592	95	below_threshold
Mycobacteroides chelonae	strain=ATCC 35752	GCA_001942545.1	1774	1774	suspected-type	True	87.4168	1378	1592	95	below_threshold
[Mycobacterium] chelonae subsp. chelonae	strain=DSM 43804	GCA_004355245.1	2099321	1774	type	True	87.394	1384	1592	95	below_threshold
Mycobacteroides chelonae	strain=CCUG 47445	GCA_001632805.1	1774	1774	suspected-type	True	87.3694	1386	1592	95	below_threshold
Mycobacteroides franklinii	strain=CV002	GCA_002013895.1	948102	948102	type	True	85.5876	1324	1592	95	below_threshold
Mycobacteroides franklinii	strain=DSM 45524	GCA_004355025.1	948102	948102	type	True	85.5723	1328	1592	95	below_threshold
Mycobacteroides franklinii	strain=DSM 45524	GCA_002086225.1	948102	948102	type	True	85.5456	1324	1592	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:32,695] [INFO] DFAST Taxonomy check result was written to GCF_004924335.1_ASM492433v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:32,696] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:32,696] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:32,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90e13bf0-d49a-400b-a7e8-1b75751719e4/dqc_reference/checkm_data
[2024-01-24 14:39:32,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:32,749] [INFO] Task started: CheckM
[2024-01-24 14:39:32,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004924335.1_ASM492433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004924335.1_ASM492433v1_genomic.fna/checkm_input GCF_004924335.1_ASM492433v1_genomic.fna/checkm_result
[2024-01-24 14:40:47,536] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:47,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:47,559] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:47,559] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:47,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004924335.1_ASM492433v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:47,560] [INFO] Task started: Blastn
[2024-01-24 14:40:47,560] [INFO] Running command: blastn -query GCF_004924335.1_ASM492433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90e13bf0-d49a-400b-a7e8-1b75751719e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_004924335.1_ASM492433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:49,107] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:49,111] [INFO] Selected 7 target genomes.
[2024-01-24 14:40:49,111] [INFO] Target genome list was writen to GCF_004924335.1_ASM492433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:49,117] [INFO] Task started: fastANI
[2024-01-24 14:40:49,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg08dbd542-293b-4e2e-9299-329de02b871c/GCF_004924335.1_ASM492433v1_genomic.fna.gz --refList GCF_004924335.1_ASM492433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004924335.1_ASM492433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:57,894] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:57,902] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:57,902] [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_004924335.1	s__Mycobacterium salmoniphilum	100.0	1592	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.49	96.58	0.95	0.92	5	conclusive
GCF_002013415.1	s__Mycobacterium sp002013415	93.0159	1386	1592	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	92.8281	1424	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.45	95.17	0.93	0.91	7	-
GCF_002013375.1	s__Mycobacterium sp002013375	92.2576	1452	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.45	98.92	0.97	0.95	3	-
GCF_002356335.1	s__Mycobacterium stephanolepidis	87.8568	1374	1592	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	87.3731	1386	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.73	95.27	0.90	0.84	73	-
GCF_002013895.1	s__Mycobacterium franklinii	85.5661	1327	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.20	95.66	0.94	0.87	12	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:57,904] [INFO] GTDB search result was written to GCF_004924335.1_ASM492433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:57,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:57,910] [INFO] DFAST_QC result json was written to GCF_004924335.1_ASM492433v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:57,910] [INFO] DFAST_QC completed!
[2024-01-24 14:40:57,911] [INFO] Total running time: 0h2m9s