[2024-01-24 13:49:30,749] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:30,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:30,751] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf17cb8b-3457-406e-aae5-3d5b9c2468f2/dqc_reference
[2024-01-24 13:49:32,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:32,063] [INFO] Task started: Prodigal
[2024-01-24 13:49:32,063] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c83eba5-3e65-407c-8722-9f17b0277a13/GCF_001942545.1_ASM194254v1_genomic.fna.gz | prodigal -d GCF_001942545.1_ASM194254v1_genomic.fna/cds.fna -a GCF_001942545.1_ASM194254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:50,297] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:50,297] [INFO] Task started: HMMsearch
[2024-01-24 13:49:50,297] [INFO] Running command: hmmsearch --tblout GCF_001942545.1_ASM194254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf17cb8b-3457-406e-aae5-3d5b9c2468f2/dqc_reference/reference_markers.hmm GCF_001942545.1_ASM194254v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:50,637] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:50,639] [INFO] Found 6/6 markers.
[2024-01-24 13:49:50,691] [INFO] Query marker FASTA was written to GCF_001942545.1_ASM194254v1_genomic.fna/markers.fasta
[2024-01-24 13:49:50,692] [INFO] Task started: Blastn
[2024-01-24 13:49:50,692] [INFO] Running command: blastn -query GCF_001942545.1_ASM194254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf17cb8b-3457-406e-aae5-3d5b9c2468f2/dqc_reference/reference_markers.fasta -out GCF_001942545.1_ASM194254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:51,812] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:51,815] [INFO] Selected 5 target genomes.
[2024-01-24 13:49:51,816] [INFO] Target genome list was writen to GCF_001942545.1_ASM194254v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:51,818] [INFO] Task started: fastANI
[2024-01-24 13:49:51,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c83eba5-3e65-407c-8722-9f17b0277a13/GCF_001942545.1_ASM194254v1_genomic.fna.gz --refList GCF_001942545.1_ASM194254v1_genomic.fna/target_genomes.txt --output GCF_001942545.1_ASM194254v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:58,224] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:58,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf17cb8b-3457-406e-aae5-3d5b9c2468f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:58,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf17cb8b-3457-406e-aae5-3d5b9c2468f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:58,232] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:49:58,232] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:58,233] [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_001942545.1	1774	1774	suspected-type	True	100.0	1674	1674	95	conclusive
[Mycobacterium] chelonae subsp. chelonae	strain=DSM 43804	GCA_004355245.1	2099321	1774	type	True	99.9992	1673	1674	95	conclusive
Mycobacteroides chelonae	strain=ATCC 35752	GCA_002102055.1	1774	1774	suspected-type	True	99.9978	1665	1674	95	conclusive
Mycobacteroides chelonae	strain=CCUG 47445	GCA_001632805.1	1774	1774	suspected-type	True	99.9974	1673	1674	95	conclusive
Mycobacteroides chelonae	strain=ATCC 35752	GCA_000971805.1	1774	1774	suspected-type	True	99.9918	1629	1674	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:49:58,240] [INFO] DFAST Taxonomy check result was written to GCF_001942545.1_ASM194254v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:58,241] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:58,242] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:58,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf17cb8b-3457-406e-aae5-3d5b9c2468f2/dqc_reference/checkm_data
[2024-01-24 13:49:58,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:58,297] [INFO] Task started: CheckM
[2024-01-24 13:49:58,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001942545.1_ASM194254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001942545.1_ASM194254v1_genomic.fna/checkm_input GCF_001942545.1_ASM194254v1_genomic.fna/checkm_result
[2024-01-24 13:50:51,939] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:51,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:51,971] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:51,971] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:51,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001942545.1_ASM194254v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:51,972] [INFO] Task started: Blastn
[2024-01-24 13:50:51,973] [INFO] Running command: blastn -query GCF_001942545.1_ASM194254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf17cb8b-3457-406e-aae5-3d5b9c2468f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001942545.1_ASM194254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:53,533] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:53,536] [INFO] Selected 9 target genomes.
[2024-01-24 13:50:53,536] [INFO] Target genome list was writen to GCF_001942545.1_ASM194254v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:53,544] [INFO] Task started: fastANI
[2024-01-24 13:50:53,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c83eba5-3e65-407c-8722-9f17b0277a13/GCF_001942545.1_ASM194254v1_genomic.fna.gz --refList GCF_001942545.1_ASM194254v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001942545.1_ASM194254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:04,349] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:04,363] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:04,363] [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	99.9974	1673	1674	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	93.8215	1447	1674	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	87.57	1380	1674	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	87.5093	1393	1674	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	87.4814	1394	1674	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	87.4007	1344	1674	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	85.524	1338	1674	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	85.0871	1098	1674	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	85.0534	1328	1674	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 13:51:04,365] [INFO] GTDB search result was written to GCF_001942545.1_ASM194254v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:04,366] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:04,368] [INFO] DFAST_QC result json was written to GCF_001942545.1_ASM194254v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:04,368] [INFO] DFAST_QC completed!
[2024-01-24 13:51:04,368] [INFO] Total running time: 0h1m34s