[2024-01-24 14:55:33,807] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:33,820] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:33,821] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9c9ecaf-e254-47af-afe8-f9a528dfad9f/dqc_reference
[2024-01-24 14:55:35,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:35,103] [INFO] Task started: Prodigal
[2024-01-24 14:55:35,103] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3b04d94-e43f-4223-96d9-f6c78b47d918/GCF_004355245.1_ASM435524v1_genomic.fna.gz | prodigal -d GCF_004355245.1_ASM435524v1_genomic.fna/cds.fna -a GCF_004355245.1_ASM435524v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:01,590] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:01,590] [INFO] Task started: HMMsearch
[2024-01-24 14:56:01,590] [INFO] Running command: hmmsearch --tblout GCF_004355245.1_ASM435524v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9c9ecaf-e254-47af-afe8-f9a528dfad9f/dqc_reference/reference_markers.hmm GCF_004355245.1_ASM435524v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:01,914] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:01,915] [INFO] Found 6/6 markers.
[2024-01-24 14:56:01,964] [INFO] Query marker FASTA was written to GCF_004355245.1_ASM435524v1_genomic.fna/markers.fasta
[2024-01-24 14:56:01,965] [INFO] Task started: Blastn
[2024-01-24 14:56:01,965] [INFO] Running command: blastn -query GCF_004355245.1_ASM435524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9c9ecaf-e254-47af-afe8-f9a528dfad9f/dqc_reference/reference_markers.fasta -out GCF_004355245.1_ASM435524v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:03,078] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:03,082] [INFO] Selected 5 target genomes.
[2024-01-24 14:56:03,082] [INFO] Target genome list was writen to GCF_004355245.1_ASM435524v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:03,088] [INFO] Task started: fastANI
[2024-01-24 14:56:03,089] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3b04d94-e43f-4223-96d9-f6c78b47d918/GCF_004355245.1_ASM435524v1_genomic.fna.gz --refList GCF_004355245.1_ASM435524v1_genomic.fna/target_genomes.txt --output GCF_004355245.1_ASM435524v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:09,421] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:09,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9c9ecaf-e254-47af-afe8-f9a528dfad9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:09,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9c9ecaf-e254-47af-afe8-f9a528dfad9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:09,433] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:56:09,433] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:09,434] [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] chelonae subsp. chelonae	strain=DSM 43804	GCA_004355245.1	2099321	1774	type	True	100.0	1675	1676	95	conclusive
Mycobacteroides chelonae	strain=ATCC 35752	GCA_001942545.1	1774	1774	suspected-type	True	99.9988	1670	1676	95	conclusive
Mycobacteroides chelonae	strain=CCUG 47445	GCA_001632805.1	1774	1774	suspected-type	True	99.9971	1676	1676	95	conclusive
Mycobacteroides chelonae	strain=ATCC 35752	GCA_002102055.1	1774	1774	suspected-type	True	99.9937	1668	1676	95	conclusive
Mycobacteroides chelonae	strain=ATCC 35752	GCA_000971805.1	1774	1774	suspected-type	True	99.9852	1632	1676	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:56:09,435] [INFO] DFAST Taxonomy check result was written to GCF_004355245.1_ASM435524v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:09,436] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:09,436] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:09,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9c9ecaf-e254-47af-afe8-f9a528dfad9f/dqc_reference/checkm_data
[2024-01-24 14:56:09,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:09,488] [INFO] Task started: CheckM
[2024-01-24 14:56:09,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004355245.1_ASM435524v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004355245.1_ASM435524v1_genomic.fna/checkm_input GCF_004355245.1_ASM435524v1_genomic.fna/checkm_result
[2024-01-24 14:57:21,394] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:21,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:21,419] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:21,420] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:21,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004355245.1_ASM435524v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:21,420] [INFO] Task started: Blastn
[2024-01-24 14:57:21,421] [INFO] Running command: blastn -query GCF_004355245.1_ASM435524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9c9ecaf-e254-47af-afe8-f9a528dfad9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004355245.1_ASM435524v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:23,267] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:23,271] [INFO] Selected 9 target genomes.
[2024-01-24 14:57:23,271] [INFO] Target genome list was writen to GCF_004355245.1_ASM435524v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:23,280] [INFO] Task started: fastANI
[2024-01-24 14:57:23,280] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3b04d94-e43f-4223-96d9-f6c78b47d918/GCF_004355245.1_ASM435524v1_genomic.fna.gz --refList GCF_004355245.1_ASM435524v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004355245.1_ASM435524v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:34,618] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:34,630] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:34,630] [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	99.9971	1676	1676	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	93.854	1446	1676	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	87.5792	1377	1676	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	87.444	1400	1676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.45	98.92	0.97	0.95	3	-
GCF_004924335.1	s__Mycobacterium salmoniphilum	87.4289	1400	1676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.49	96.58	0.95	0.92	5	-
GCF_002013415.1	s__Mycobacterium sp002013415	87.377	1335	1676	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	85.5013	1321	1676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.82	98.51	0.95	0.95	4	-
GCF_014204435.1	s__Mycobacterium chelonae_A	85.1024	1102	1676	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002013895.1	s__Mycobacterium franklinii	85.0921	1305	1676	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 14:57:34,632] [INFO] GTDB search result was written to GCF_004355245.1_ASM435524v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:34,633] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:34,635] [INFO] DFAST_QC result json was written to GCF_004355245.1_ASM435524v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:34,636] [INFO] DFAST_QC completed!
[2024-01-24 14:57:34,636] [INFO] Total running time: 0h2m1s