[2024-01-24 13:43:26,853] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:26,855] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:26,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cc37f69-ae73-42e4-8cbc-84169af17957/dqc_reference
[2024-01-24 13:43:28,053] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:28,054] [INFO] Task started: Prodigal
[2024-01-24 13:43:28,054] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8b070cf-fd8e-4ee3-b283-1283ccec5de3/GCF_009026825.1_ASM902682v1_genomic.fna.gz | prodigal -d GCF_009026825.1_ASM902682v1_genomic.fna/cds.fna -a GCF_009026825.1_ASM902682v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:35,483] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:35,483] [INFO] Task started: HMMsearch
[2024-01-24 13:43:35,483] [INFO] Running command: hmmsearch --tblout GCF_009026825.1_ASM902682v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cc37f69-ae73-42e4-8cbc-84169af17957/dqc_reference/reference_markers.hmm GCF_009026825.1_ASM902682v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:35,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:35,652] [INFO] Found 6/6 markers.
[2024-01-24 13:43:35,674] [INFO] Query marker FASTA was written to GCF_009026825.1_ASM902682v1_genomic.fna/markers.fasta
[2024-01-24 13:43:35,674] [INFO] Task started: Blastn
[2024-01-24 13:43:35,674] [INFO] Running command: blastn -query GCF_009026825.1_ASM902682v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc37f69-ae73-42e4-8cbc-84169af17957/dqc_reference/reference_markers.fasta -out GCF_009026825.1_ASM902682v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:36,532] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:36,535] [INFO] Selected 17 target genomes.
[2024-01-24 13:43:36,535] [INFO] Target genome list was writen to GCF_009026825.1_ASM902682v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:36,561] [INFO] Task started: fastANI
[2024-01-24 13:43:36,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8b070cf-fd8e-4ee3-b283-1283ccec5de3/GCF_009026825.1_ASM902682v1_genomic.fna.gz --refList GCF_009026825.1_ASM902682v1_genomic.fna/target_genomes.txt --output GCF_009026825.1_ASM902682v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:43,519] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:43,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cc37f69-ae73-42e4-8cbc-84169af17957/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:43,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cc37f69-ae73-42e4-8cbc-84169af17957/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:43,533] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:43,533] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:43,534] [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 urogenitale	strain=LMM-1652	GCA_009026825.1	2487892	2487892	type	True	100.0	781	783	95	conclusive
Corynebacterium ureicelerivorans	strain=IMMIB RIV-2301	GCA_000747315.1	401472	401472	type	True	79.4876	97	783	95	below_threshold
Corynebacterium falsenii	strain=FDAARGOS_1494	GCA_020099275.1	108486	108486	type	True	79.3496	245	783	95	below_threshold
Corynebacterium dentalis	strain=Marseille-P4122	GCA_900232865.1	2014528	2014528	type	True	79.3092	289	783	95	below_threshold
Corynebacterium jeikeium	strain=NCTC11913	GCA_900461185.1	38289	38289	suspected-type	True	79.3056	235	783	95	below_threshold
Corynebacterium mucifaciens	strain=ATCC 700355	GCA_012396315.1	57171	57171	type	True	79.0553	97	783	95	below_threshold
Corynebacterium auriscanis	strain=CIP 106629	GCA_000767255.1	99807	99807	type	True	79.0541	157	783	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_000163435.1	38289	38289	suspected-type	True	78.9882	238	783	95	below_threshold
Corynebacterium resistens	strain=DSM 45100	GCA_000177535.2	258224	258224	type	True	78.9779	174	783	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_001999385.1	38289	38289	suspected-type	True	78.9333	232	783	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	78.9333	204	783	95	below_threshold
Corynebacterium urealyticum	strain=NCTC12011	GCA_900187235.1	43771	43771	type	True	78.895	201	783	95	below_threshold
Corynebacterium zhongnanshanii	strain=zg-320	GCA_014490575.1	2768834	2768834	type	True	78.8671	197	783	95	below_threshold
Corynebacterium urealyticum	strain=DSM 7109	GCA_000069945.1	43771	43771	type	True	78.7626	202	783	95	below_threshold
Corynebacterium suicordis	strain=DSM 45110	GCA_015351405.1	203264	203264	type	True	78.7243	253	783	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	78.5306	120	783	95	below_threshold
Corynebacterium kalinowskii	strain=1959	GCA_009734385.1	2675216	2675216	type	True	77.9336	115	783	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:43,535] [INFO] DFAST Taxonomy check result was written to GCF_009026825.1_ASM902682v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:43,536] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:43,536] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:43,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cc37f69-ae73-42e4-8cbc-84169af17957/dqc_reference/checkm_data
[2024-01-24 13:43:43,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:43,562] [INFO] Task started: CheckM
[2024-01-24 13:43:43,562] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009026825.1_ASM902682v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009026825.1_ASM902682v1_genomic.fna/checkm_input GCF_009026825.1_ASM902682v1_genomic.fna/checkm_result
[2024-01-24 13:44:09,695] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:09,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:09,715] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:09,715] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:09,715] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009026825.1_ASM902682v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:09,716] [INFO] Task started: Blastn
[2024-01-24 13:44:09,716] [INFO] Running command: blastn -query GCF_009026825.1_ASM902682v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc37f69-ae73-42e4-8cbc-84169af17957/dqc_reference/reference_markers_gtdb.fasta -out GCF_009026825.1_ASM902682v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:10,851] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:10,854] [INFO] Selected 15 target genomes.
[2024-01-24 13:44:10,854] [INFO] Target genome list was writen to GCF_009026825.1_ASM902682v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:10,870] [INFO] Task started: fastANI
[2024-01-24 13:44:10,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8b070cf-fd8e-4ee3-b283-1283ccec5de3/GCF_009026825.1_ASM902682v1_genomic.fna.gz --refList GCF_009026825.1_ASM902682v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009026825.1_ASM902682v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:17,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:17,325] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:17,325] [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_009026825.1	s__Corynebacterium sp009026825	100.0	781	783	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_000738175.1	s__Corynebacterium jeikeium_C	79.3814	246	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000525655.1	s__Corynebacterium falsenii	79.3306	254	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.72	98.72	0.95	0.95	2	-
GCF_900232865.1	s__Corynebacterium dentalis	79.3009	290	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.56	98.56	0.96	0.96	2	-
GCF_000738265.1	s__Corynebacterium jeikeium_A	79.236	242	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.92	97.52	0.95	0.93	11	-
GCF_001807485.1	s__Corynebacterium sp001807485	79.1571	249	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCF_000767255.1	s__Corynebacterium auriscanis	79.0697	156	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.87	97.87	0.94	0.94	2	-
GCF_000163435.1	s__Corynebacterium jeikeium	79.0056	237	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.68	96.00	0.93	0.90	9	-
GCF_000177535.2	s__Corynebacterium resistens	78.7928	171	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000069945.1	s__Corynebacterium urealyticum	78.7843	201	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.66	97.50	0.94	0.89	9	-
GCF_015351405.1	s__Corynebacterium sp015351405	78.7411	252	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001815985.1	s__Corynebacterium sp001815985	78.7286	184	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.95	96.87	0.95	0.94	3	-
GCA_019120635.1	s__Corynebacterium intestinavium	78.5723	179	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114175.1	s__Corynebacterium gallistercoris	78.42	219	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734385.1	s__Corynebacterium sp009734385	77.9154	114	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:17,327] [INFO] GTDB search result was written to GCF_009026825.1_ASM902682v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:17,327] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:17,330] [INFO] DFAST_QC result json was written to GCF_009026825.1_ASM902682v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:17,331] [INFO] DFAST_QC completed!
[2024-01-24 13:44:17,331] [INFO] Total running time: 0h0m50s