[2024-01-25 18:45:05,521] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:05,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:05,522] [INFO] DQC Reference Directory: /var/lib/cwl/stgd91d7360-a8ee-4d2f-8772-cacf1a3fb1ab/dqc_reference
[2024-01-25 18:45:06,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:06,687] [INFO] Task started: Prodigal
[2024-01-25 18:45:06,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg780f8cd9-6677-4248-8d3a-c689839d8c8e/GCF_009734385.1_ASM973438v1_genomic.fna.gz | prodigal -d GCF_009734385.1_ASM973438v1_genomic.fna/cds.fna -a GCF_009734385.1_ASM973438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:14,831] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:14,831] [INFO] Task started: HMMsearch
[2024-01-25 18:45:14,831] [INFO] Running command: hmmsearch --tblout GCF_009734385.1_ASM973438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd91d7360-a8ee-4d2f-8772-cacf1a3fb1ab/dqc_reference/reference_markers.hmm GCF_009734385.1_ASM973438v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:15,044] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:15,045] [INFO] Found 6/6 markers.
[2024-01-25 18:45:15,077] [INFO] Query marker FASTA was written to GCF_009734385.1_ASM973438v1_genomic.fna/markers.fasta
[2024-01-25 18:45:15,077] [INFO] Task started: Blastn
[2024-01-25 18:45:15,077] [INFO] Running command: blastn -query GCF_009734385.1_ASM973438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd91d7360-a8ee-4d2f-8772-cacf1a3fb1ab/dqc_reference/reference_markers.fasta -out GCF_009734385.1_ASM973438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:15,877] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:15,880] [INFO] Selected 13 target genomes.
[2024-01-25 18:45:15,880] [INFO] Target genome list was writen to GCF_009734385.1_ASM973438v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:15,894] [INFO] Task started: fastANI
[2024-01-25 18:45:15,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg780f8cd9-6677-4248-8d3a-c689839d8c8e/GCF_009734385.1_ASM973438v1_genomic.fna.gz --refList GCF_009734385.1_ASM973438v1_genomic.fna/target_genomes.txt --output GCF_009734385.1_ASM973438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:22,033] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:22,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd91d7360-a8ee-4d2f-8772-cacf1a3fb1ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:22,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd91d7360-a8ee-4d2f-8772-cacf1a3fb1ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:22,042] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:45:22,042] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:45:22,042] [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
Corynebacterium kalinowskii	strain=1959	GCA_009734385.1	2675216	2675216	type	True	100.0	836	836	95	conclusive
Corynebacterium hindlerae	strain=NML 93-0612	GCA_014117265.1	699041	699041	type	True	80.3278	366	836	95	below_threshold
Corynebacterium epidermidicanis	strain=DSM 45586	GCA_001021025.1	1050174	1050174	type	True	79.3749	261	836	95	below_threshold
Corynebacterium deserti	strain=GIMN1.010	GCA_001277995.1	1408191	1408191	type	True	78.7412	140	836	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.4675	213	836	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	78.3945	159	836	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.0486	206	836	95	below_threshold
Corynebacterium uterequi	strain=DSM 45634	GCA_001021065.1	1072256	1072256	type	True	77.6781	114	836	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	77.6721	189	836	95	below_threshold
Corynebacterium doosanense	strain=CAU 212	GCA_000767055.1	1121358	1121358	type	True	77.6379	151	836	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	77.6278	195	836	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	77.5287	144	836	95	below_threshold
Corynebacterium doosanense	strain=DSM 45436	GCA_000372245.1	1121358	1121358	type	True	77.0796	149	836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:22,044] [INFO] DFAST Taxonomy check result was written to GCF_009734385.1_ASM973438v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:22,044] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:22,044] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:22,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd91d7360-a8ee-4d2f-8772-cacf1a3fb1ab/dqc_reference/checkm_data
[2024-01-25 18:45:22,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:22,072] [INFO] Task started: CheckM
[2024-01-25 18:45:22,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009734385.1_ASM973438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009734385.1_ASM973438v1_genomic.fna/checkm_input GCF_009734385.1_ASM973438v1_genomic.fna/checkm_result
[2024-01-25 18:45:50,550] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:50,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:50,577] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:50,577] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:50,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009734385.1_ASM973438v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:50,577] [INFO] Task started: Blastn
[2024-01-25 18:45:50,577] [INFO] Running command: blastn -query GCF_009734385.1_ASM973438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd91d7360-a8ee-4d2f-8772-cacf1a3fb1ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_009734385.1_ASM973438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:51,738] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:51,741] [INFO] Selected 14 target genomes.
[2024-01-25 18:45:51,741] [INFO] Target genome list was writen to GCF_009734385.1_ASM973438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:51,766] [INFO] Task started: fastANI
[2024-01-25 18:45:51,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg780f8cd9-6677-4248-8d3a-c689839d8c8e/GCF_009734385.1_ASM973438v1_genomic.fna.gz --refList GCF_009734385.1_ASM973438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009734385.1_ASM973438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:58,734] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:58,743] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:58,743] [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_009734385.1	s__Corynebacterium sp009734385	100.0	836	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014117265.1	s__Corynebacterium sp014117265	80.3727	367	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.31	97.31	0.93	0.93	2	-
GCF_001021025.1	s__Corynebacterium epidermidicanis	79.4354	260	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001277995.1	s__Corynebacterium deserti	78.8127	140	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.5445	212	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_009734425.1	s__Corynebacterium sp009734425	78.3921	160	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009026825.1	s__Corynebacterium sp009026825	78.1339	115	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819445.1	s__Corynebacterium humireducens	78.1018	205	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_900177745.1	s__Corynebacterium pollutisoli	77.6896	188	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_000767055.1	s__Corynebacterium doosanense	77.6361	150	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001941485.1	s__Corynebacterium frankenforstense	77.6252	145	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994655.1	s__Corynebacterium sp002994655	77.5638	168	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017942225.1	s__Corynebacterium sp017942225	77.3346	108	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838985.1	s__Corynebacterium sp012838985	77.0709	154	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:58,745] [INFO] GTDB search result was written to GCF_009734385.1_ASM973438v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:58,745] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:58,748] [INFO] DFAST_QC result json was written to GCF_009734385.1_ASM973438v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:58,748] [INFO] DFAST_QC completed!
[2024-01-25 18:45:58,748] [INFO] Total running time: 0h0m53s