[2024-01-25 20:12:20,553] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:20,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:20,555] [INFO] DQC Reference Directory: /var/lib/cwl/stga1cf414d-287b-4ab8-8f68-3597ed891e6b/dqc_reference
[2024-01-25 20:12:21,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:21,687] [INFO] Task started: Prodigal
[2024-01-25 20:12:21,687] [INFO] Running command: gunzip -c /var/lib/cwl/stgd361857d-0e3d-4d06-94c0-2d17f5d109d9/GCF_002013685.1_ASM201368v1_genomic.fna.gz | prodigal -d GCF_002013685.1_ASM201368v1_genomic.fna/cds.fna -a GCF_002013685.1_ASM201368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:37,377] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:37,378] [INFO] Task started: HMMsearch
[2024-01-25 20:12:37,378] [INFO] Running command: hmmsearch --tblout GCF_002013685.1_ASM201368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1cf414d-287b-4ab8-8f68-3597ed891e6b/dqc_reference/reference_markers.hmm GCF_002013685.1_ASM201368v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:37,621] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:37,622] [INFO] Found 6/6 markers.
[2024-01-25 20:12:37,692] [INFO] Query marker FASTA was written to GCF_002013685.1_ASM201368v1_genomic.fna/markers.fasta
[2024-01-25 20:12:37,692] [INFO] Task started: Blastn
[2024-01-25 20:12:37,692] [INFO] Running command: blastn -query GCF_002013685.1_ASM201368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1cf414d-287b-4ab8-8f68-3597ed891e6b/dqc_reference/reference_markers.fasta -out GCF_002013685.1_ASM201368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:38,704] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:38,707] [INFO] Selected 10 target genomes.
[2024-01-25 20:12:38,707] [INFO] Target genome list was writen to GCF_002013685.1_ASM201368v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:38,713] [INFO] Task started: fastANI
[2024-01-25 20:12:38,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgd361857d-0e3d-4d06-94c0-2d17f5d109d9/GCF_002013685.1_ASM201368v1_genomic.fna.gz --refList GCF_002013685.1_ASM201368v1_genomic.fna/target_genomes.txt --output GCF_002013685.1_ASM201368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:49,702] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:49,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1cf414d-287b-4ab8-8f68-3597ed891e6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:49,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1cf414d-287b-4ab8-8f68-3597ed891e6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:49,711] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:12:49,711] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:49,711] [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=SC	GCA_002013685.1	404941	404941	suspected-type	True	100.0	1553	1557	95	conclusive
Mycobacteroides salmoniphilum	strain=DSM 43276	GCA_004924335.1	404941	404941	suspected-type	True	99.991	1551	1557	95	conclusive
[Mycobacterium] stephanolepidis	strain=NJB0901	GCA_002356335.1	1520670	1520670	type	True	87.8852	1353	1557	95	below_threshold
Mycobacteroides chelonae	strain=ATCC 35752	GCA_000971805.1	1774	1774	suspected-type	True	87.4634	1350	1557	95	below_threshold
Mycobacteroides chelonae	strain=CCUG 47445	GCA_001632805.1	1774	1774	suspected-type	True	87.3813	1390	1557	95	below_threshold
Mycobacteroides chelonae	strain=ATCC 35752	GCA_001942545.1	1774	1774	suspected-type	True	87.3744	1379	1557	95	below_threshold
[Mycobacterium] chelonae subsp. chelonae	strain=DSM 43804	GCA_004355245.1	2099321	1774	type	True	87.3551	1393	1557	95	below_threshold
Mycobacteroides franklinii	strain=CV002	GCA_002013895.1	948102	948102	type	True	85.6298	1295	1557	95	below_threshold
Mycobacteroides franklinii	strain=DSM 45524	GCA_002086225.1	948102	948102	type	True	85.5999	1297	1557	95	below_threshold
Mycobacteroides franklinii	strain=DSM 45524	GCA_004355025.1	948102	948102	type	True	85.5398	1322	1557	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:49,713] [INFO] DFAST Taxonomy check result was written to GCF_002013685.1_ASM201368v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:49,713] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:49,714] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:49,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1cf414d-287b-4ab8-8f68-3597ed891e6b/dqc_reference/checkm_data
[2024-01-25 20:12:49,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:49,760] [INFO] Task started: CheckM
[2024-01-25 20:12:49,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002013685.1_ASM201368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002013685.1_ASM201368v1_genomic.fna/checkm_input GCF_002013685.1_ASM201368v1_genomic.fna/checkm_result
[2024-01-25 20:13:35,263] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:35,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:35,313] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:35,313] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:35,314] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002013685.1_ASM201368v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:35,314] [INFO] Task started: Blastn
[2024-01-25 20:13:35,314] [INFO] Running command: blastn -query GCF_002013685.1_ASM201368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1cf414d-287b-4ab8-8f68-3597ed891e6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002013685.1_ASM201368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:36,787] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:36,790] [INFO] Selected 7 target genomes.
[2024-01-25 20:13:36,790] [INFO] Target genome list was writen to GCF_002013685.1_ASM201368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:36,796] [INFO] Task started: fastANI
[2024-01-25 20:13:36,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgd361857d-0e3d-4d06-94c0-2d17f5d109d9/GCF_002013685.1_ASM201368v1_genomic.fna.gz --refList GCF_002013685.1_ASM201368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002013685.1_ASM201368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:45,952] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:45,958] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:45,958] [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	99.991	1551	1557	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	92.9882	1370	1557	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	92.8701	1400	1557	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	92.2789	1405	1557	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	87.8852	1353	1557	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	87.3813	1390	1557	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	85.6166	1298	1557	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.20	95.66	0.94	0.87	12	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:45,960] [INFO] GTDB search result was written to GCF_002013685.1_ASM201368v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:45,960] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:45,963] [INFO] DFAST_QC result json was written to GCF_002013685.1_ASM201368v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:45,963] [INFO] DFAST_QC completed!
[2024-01-25 20:13:45,963] [INFO] Total running time: 0h1m25s