[2024-01-24 15:18:05,204] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:05,206] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:05,206] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bd14a6c-2b27-41a7-9f96-2098e78f12d3/dqc_reference
[2024-01-24 15:18:07,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:07,531] [INFO] Task started: Prodigal
[2024-01-24 15:18:07,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ed0b867-78fa-4f48-8985-28fe272627f9/GCF_002356335.1_ASM235633v1_genomic.fna.gz | prodigal -d GCF_002356335.1_ASM235633v1_genomic.fna/cds.fna -a GCF_002356335.1_ASM235633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:25,672] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:25,673] [INFO] Task started: HMMsearch
[2024-01-24 15:18:25,673] [INFO] Running command: hmmsearch --tblout GCF_002356335.1_ASM235633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bd14a6c-2b27-41a7-9f96-2098e78f12d3/dqc_reference/reference_markers.hmm GCF_002356335.1_ASM235633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:26,014] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:26,016] [INFO] Found 6/6 markers.
[2024-01-24 15:18:26,062] [INFO] Query marker FASTA was written to GCF_002356335.1_ASM235633v1_genomic.fna/markers.fasta
[2024-01-24 15:18:26,062] [INFO] Task started: Blastn
[2024-01-24 15:18:26,063] [INFO] Running command: blastn -query GCF_002356335.1_ASM235633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bd14a6c-2b27-41a7-9f96-2098e78f12d3/dqc_reference/reference_markers.fasta -out GCF_002356335.1_ASM235633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:27,163] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:27,168] [INFO] Selected 10 target genomes.
[2024-01-24 15:18:27,169] [INFO] Target genome list was writen to GCF_002356335.1_ASM235633v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:27,174] [INFO] Task started: fastANI
[2024-01-24 15:18:27,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ed0b867-78fa-4f48-8985-28fe272627f9/GCF_002356335.1_ASM235633v1_genomic.fna.gz --refList GCF_002356335.1_ASM235633v1_genomic.fna/target_genomes.txt --output GCF_002356335.1_ASM235633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:39,291] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:39,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bd14a6c-2b27-41a7-9f96-2098e78f12d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:39,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bd14a6c-2b27-41a7-9f96-2098e78f12d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:39,302] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:39,302] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:39,302] [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] stephanolepidis	strain=NJB0901	GCA_002356335.1	1520670	1520670	type	True	100.0	1664	1664	95	conclusive
Mycobacteroides chelonae	strain=ATCC 35752	GCA_001942545.1	1774	1774	suspected-type	True	93.8355	1448	1664	95	below_threshold
Mycobacteroides chelonae	strain=ATCC 35752	GCA_000971805.1	1774	1774	suspected-type	True	93.8269	1441	1664	95	below_threshold
Mycobacteroides chelonae	strain=ATCC 35752	GCA_002102055.1	1774	1774	suspected-type	True	93.8205	1446	1664	95	below_threshold
Mycobacteroides chelonae	strain=CCUG 47445	GCA_001632805.1	1774	1774	suspected-type	True	93.8131	1446	1664	95	below_threshold
[Mycobacterium] chelonae subsp. chelonae	strain=DSM 43804	GCA_004355245.1	2099321	1774	type	True	93.7995	1450	1664	95	below_threshold
Mycobacteroides saopaulense	strain=EPM10906	GCA_001456355.1	1578165	1578165	type	True	85.6708	1307	1664	95	below_threshold
Mycobacteroides saopaulense	strain=CCUG 66554	GCA_002086715.1	1578165	1578165	type	True	85.6167	1278	1664	95	below_threshold
Mycobacteroides franklinii	strain=DSM 45524	GCA_004355025.1	948102	948102	type	True	85.1921	1310	1664	95	below_threshold
Mycobacteroides franklinii	strain=DSM 45524	GCA_002086225.1	948102	948102	type	True	85.1661	1297	1664	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:39,304] [INFO] DFAST Taxonomy check result was written to GCF_002356335.1_ASM235633v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:39,304] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:39,305] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:39,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bd14a6c-2b27-41a7-9f96-2098e78f12d3/dqc_reference/checkm_data
[2024-01-24 15:18:39,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:39,358] [INFO] Task started: CheckM
[2024-01-24 15:18:39,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002356335.1_ASM235633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002356335.1_ASM235633v1_genomic.fna/checkm_input GCF_002356335.1_ASM235633v1_genomic.fna/checkm_result
[2024-01-24 15:19:34,389] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:34,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:34,414] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:34,414] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:34,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002356335.1_ASM235633v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:34,415] [INFO] Task started: Blastn
[2024-01-24 15:19:34,415] [INFO] Running command: blastn -query GCF_002356335.1_ASM235633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bd14a6c-2b27-41a7-9f96-2098e78f12d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002356335.1_ASM235633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:35,989] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:35,992] [INFO] Selected 9 target genomes.
[2024-01-24 15:19:35,992] [INFO] Target genome list was writen to GCF_002356335.1_ASM235633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:35,998] [INFO] Task started: fastANI
[2024-01-24 15:19:35,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ed0b867-78fa-4f48-8985-28fe272627f9/GCF_002356335.1_ASM235633v1_genomic.fna.gz --refList GCF_002356335.1_ASM235633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002356335.1_ASM235633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:46,850] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:46,859] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:46,859] [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_002356335.1	s__Mycobacterium stephanolepidis	100.0	1664	1664	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_001632805.1	s__Mycobacterium chelonae	93.8131	1446	1664	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.73	95.27	0.90	0.84	73	-
GCF_002013465.1	s__Mycobacterium sp002013465	88.0794	1366	1664	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	87.92	1365	1664	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.49	96.58	0.95	0.92	5	-
GCF_002013375.1	s__Mycobacterium sp002013375	87.8902	1363	1664	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	87.7452	1320	1664	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	85.6708	1307	1664	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.82	98.51	0.95	0.95	4	-
GCF_002013895.1	s__Mycobacterium franklinii	85.1343	1316	1664	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.20	95.66	0.94	0.87	12	-
GCF_014204435.1	s__Mycobacterium chelonae_A	85.0868	1101	1664	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 15:19:46,860] [INFO] GTDB search result was written to GCF_002356335.1_ASM235633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:46,861] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:46,868] [INFO] DFAST_QC result json was written to GCF_002356335.1_ASM235633v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:46,868] [INFO] DFAST_QC completed!
[2024-01-24 15:19:46,868] [INFO] Total running time: 0h1m42s