[2024-01-24 11:30:49,413] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:30:49,415] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:30:49,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg915c5eb0-ad07-43ba-a1b5-5272b00d5e70/dqc_reference
[2024-01-24 11:30:50,631] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:30:50,632] [INFO] Task started: Prodigal
[2024-01-24 11:30:50,632] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c226cf5-3c17-452d-bb1a-ade8a59562c5/GCF_003390495.1_ASM339049v1_genomic.fna.gz | prodigal -d GCF_003390495.1_ASM339049v1_genomic.fna/cds.fna -a GCF_003390495.1_ASM339049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:31:09,728] [INFO] Task succeeded: Prodigal
[2024-01-24 11:31:09,729] [INFO] Task started: HMMsearch
[2024-01-24 11:31:09,729] [INFO] Running command: hmmsearch --tblout GCF_003390495.1_ASM339049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg915c5eb0-ad07-43ba-a1b5-5272b00d5e70/dqc_reference/reference_markers.hmm GCF_003390495.1_ASM339049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:31:10,004] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:31:10,005] [INFO] Found 6/6 markers.
[2024-01-24 11:31:10,049] [INFO] Query marker FASTA was written to GCF_003390495.1_ASM339049v1_genomic.fna/markers.fasta
[2024-01-24 11:31:10,050] [INFO] Task started: Blastn
[2024-01-24 11:31:10,050] [INFO] Running command: blastn -query GCF_003390495.1_ASM339049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg915c5eb0-ad07-43ba-a1b5-5272b00d5e70/dqc_reference/reference_markers.fasta -out GCF_003390495.1_ASM339049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:11,164] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:11,167] [INFO] Selected 5 target genomes.
[2024-01-24 11:31:11,168] [INFO] Target genome list was writen to GCF_003390495.1_ASM339049v1_genomic.fna/target_genomes.txt
[2024-01-24 11:31:11,171] [INFO] Task started: fastANI
[2024-01-24 11:31:11,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c226cf5-3c17-452d-bb1a-ade8a59562c5/GCF_003390495.1_ASM339049v1_genomic.fna.gz --refList GCF_003390495.1_ASM339049v1_genomic.fna/target_genomes.txt --output GCF_003390495.1_ASM339049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:31:17,266] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:17,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg915c5eb0-ad07-43ba-a1b5-5272b00d5e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:31:17,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg915c5eb0-ad07-43ba-a1b5-5272b00d5e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:31:17,280] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:31:17,280] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:31:17,280] [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 chelonae	strain=ATCC 35752	GCA_000971805.1	1774	1774	suspected-type	True	95.7172	1475	1702	95	conclusive
Mycobacteroides chelonae	strain=ATCC 35752	GCA_002102055.1	1774	1774	suspected-type	True	95.6749	1493	1702	95	conclusive
Mycobacteroides chelonae	strain=ATCC 35752	GCA_001942545.1	1774	1774	suspected-type	True	95.661	1494	1702	95	conclusive
Mycobacteroides chelonae	strain=CCUG 47445	GCA_001632805.1	1774	1774	suspected-type	True	95.6198	1502	1702	95	conclusive
[Mycobacterium] chelonae subsp. chelonae	strain=DSM 43804	GCA_004355245.1	2099321	1774	type	True	95.6111	1509	1702	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:31:17,282] [INFO] DFAST Taxonomy check result was written to GCF_003390495.1_ASM339049v1_genomic.fna/tc_result.tsv
[2024-01-24 11:31:17,283] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:31:17,283] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:31:17,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg915c5eb0-ad07-43ba-a1b5-5272b00d5e70/dqc_reference/checkm_data
[2024-01-24 11:31:17,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:31:17,335] [INFO] Task started: CheckM
[2024-01-24 11:31:17,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003390495.1_ASM339049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003390495.1_ASM339049v1_genomic.fna/checkm_input GCF_003390495.1_ASM339049v1_genomic.fna/checkm_result
[2024-01-24 11:32:13,223] [INFO] Task succeeded: CheckM
[2024-01-24 11:32:13,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:32:13,247] [INFO] ===== Completeness check finished =====
[2024-01-24 11:32:13,247] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:32:13,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003390495.1_ASM339049v1_genomic.fna/markers.fasta)
[2024-01-24 11:32:13,248] [INFO] Task started: Blastn
[2024-01-24 11:32:13,248] [INFO] Running command: blastn -query GCF_003390495.1_ASM339049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg915c5eb0-ad07-43ba-a1b5-5272b00d5e70/dqc_reference/reference_markers_gtdb.fasta -out GCF_003390495.1_ASM339049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:32:14,825] [INFO] Task succeeded: Blastn
[2024-01-24 11:32:14,830] [INFO] Selected 9 target genomes.
[2024-01-24 11:32:14,830] [INFO] Target genome list was writen to GCF_003390495.1_ASM339049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:32:14,836] [INFO] Task started: fastANI
[2024-01-24 11:32:14,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c226cf5-3c17-452d-bb1a-ade8a59562c5/GCF_003390495.1_ASM339049v1_genomic.fna.gz --refList GCF_003390495.1_ASM339049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003390495.1_ASM339049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:32:26,835] [INFO] Task succeeded: fastANI
[2024-01-24 11:32:26,852] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:32:26,853] [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_001632805.1	s__Mycobacterium chelonae	95.6198	1502	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.73	95.27	0.90	0.84	73	conclusive
GCF_002356335.1	s__Mycobacterium stephanolepidis	93.9666	1454	1702	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002013465.1	s__Mycobacterium sp002013465	87.6915	1374	1702	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	87.4981	1398	1702	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	87.4944	1381	1702	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	87.4439	1338	1702	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	85.5269	1341	1702	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	85.1594	1306	1702	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	84.977	1112	1702	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 11:32:26,855] [INFO] GTDB search result was written to GCF_003390495.1_ASM339049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:32:26,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:32:26,859] [INFO] DFAST_QC result json was written to GCF_003390495.1_ASM339049v1_genomic.fna/dqc_result.json
[2024-01-24 11:32:26,860] [INFO] DFAST_QC completed!
[2024-01-24 11:32:26,860] [INFO] Total running time: 0h1m37s