[2024-01-24 11:20:49,952] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:49,954] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:49,955] [INFO] DQC Reference Directory: /var/lib/cwl/stg31ae9d18-562f-4ce1-91e3-c96a869b4799/dqc_reference
[2024-01-24 11:20:51,129] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:51,130] [INFO] Task started: Prodigal
[2024-01-24 11:20:51,130] [INFO] Running command: gunzip -c /var/lib/cwl/stgba2fa04b-ed1b-4f46-a895-848e9d974832/GCF_030408675.1_ASM3040867v1_genomic.fna.gz | prodigal -d GCF_030408675.1_ASM3040867v1_genomic.fna/cds.fna -a GCF_030408675.1_ASM3040867v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:00,951] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:00,952] [INFO] Task started: HMMsearch
[2024-01-24 11:21:00,952] [INFO] Running command: hmmsearch --tblout GCF_030408675.1_ASM3040867v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31ae9d18-562f-4ce1-91e3-c96a869b4799/dqc_reference/reference_markers.hmm GCF_030408675.1_ASM3040867v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:01,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:01,188] [INFO] Found 6/6 markers.
[2024-01-24 11:21:01,216] [INFO] Query marker FASTA was written to GCF_030408675.1_ASM3040867v1_genomic.fna/markers.fasta
[2024-01-24 11:21:01,216] [INFO] Task started: Blastn
[2024-01-24 11:21:01,216] [INFO] Running command: blastn -query GCF_030408675.1_ASM3040867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31ae9d18-562f-4ce1-91e3-c96a869b4799/dqc_reference/reference_markers.fasta -out GCF_030408675.1_ASM3040867v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:02,070] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:02,074] [INFO] Selected 23 target genomes.
[2024-01-24 11:21:02,075] [INFO] Target genome list was writen to GCF_030408675.1_ASM3040867v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:02,181] [INFO] Task started: fastANI
[2024-01-24 11:21:02,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgba2fa04b-ed1b-4f46-a895-848e9d974832/GCF_030408675.1_ASM3040867v1_genomic.fna.gz --refList GCF_030408675.1_ASM3040867v1_genomic.fna/target_genomes.txt --output GCF_030408675.1_ASM3040867v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:11,602] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:11,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31ae9d18-562f-4ce1-91e3-c96a869b4799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:11,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31ae9d18-562f-4ce1-91e3-c96a869b4799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:11,624] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:11,624] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:11,624] [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 durum	strain=DSM 45333	GCA_013410305.1	61592	61592	type	True	99.9992	928	928	95	conclusive
Corynebacterium argentoratense	strain=DSM 44202	GCA_000590555.1	42817	42817	type	True	78.8824	114	928	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_002847405.1	1718	1718	type	True	78.7161	92	928	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.6597	139	928	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032 substr. K051	GCA_000382905.1	1718	1718	type	True	78.6352	91	928	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.5166	139	928	95	below_threshold
Corynebacterium kalinowskii	strain=1959	GCA_009734385.1	2675216	2675216	type	True	78.5005	109	928	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_000011325.1	1718	1718	type	True	78.28	89	928	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	78.2082	119	928	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.1676	117	928	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.0557	117	928	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	77.9292	88	928	95	below_threshold
Corynebacterium canis	strain=CCUG 58627	GCA_007859215.1	679663	679663	type	True	77.7633	146	928	95	below_threshold
Corynebacterium silvaticum	strain=KL0182	GCA_004382825.2	2320431	2320431	type	True	77.6827	73	928	95	below_threshold
Corynebacterium timonense	strain=DSM 45434	GCA_900105305.1	441500	441500	type	True	77.4953	82	928	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	77.3837	108	928	95	below_threshold
Corynebacterium ciconiae	strain=DSM 44920	GCA_000372385.1	227319	227319	type	True	77.3544	118	928	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	77.3513	94	928	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	77.3241	110	928	95	below_threshold
Corynebacterium timonense	strain=5401744	GCA_000312345.1	441500	441500	type	True	77.1744	79	928	95	below_threshold
Corynebacterium tapiri	strain=LMG 28165	GCA_006334925.1	1448266	1448266	type	True	77.1133	84	928	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	77.0966	77	928	95	below_threshold
Corynebacterium wankanglinii	strain=zg-913	GCA_013601005.1	2735136	2735136	type	True	76.903	75	928	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:11,626] [INFO] DFAST Taxonomy check result was written to GCF_030408675.1_ASM3040867v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:11,627] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:11,627] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:11,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31ae9d18-562f-4ce1-91e3-c96a869b4799/dqc_reference/checkm_data
[2024-01-24 11:21:11,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:11,660] [INFO] Task started: CheckM
[2024-01-24 11:21:11,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408675.1_ASM3040867v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408675.1_ASM3040867v1_genomic.fna/checkm_input GCF_030408675.1_ASM3040867v1_genomic.fna/checkm_result
[2024-01-24 11:21:44,010] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:44,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:44,033] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:44,033] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:44,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408675.1_ASM3040867v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:44,034] [INFO] Task started: Blastn
[2024-01-24 11:21:44,034] [INFO] Running command: blastn -query GCF_030408675.1_ASM3040867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31ae9d18-562f-4ce1-91e3-c96a869b4799/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408675.1_ASM3040867v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:45,264] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:45,268] [INFO] Selected 24 target genomes.
[2024-01-24 11:21:45,268] [INFO] Target genome list was writen to GCF_030408675.1_ASM3040867v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:45,300] [INFO] Task started: fastANI
[2024-01-24 11:21:45,300] [INFO] Running command: fastANI --query /var/lib/cwl/stgba2fa04b-ed1b-4f46-a895-848e9d974832/GCF_030408675.1_ASM3040867v1_genomic.fna.gz --refList GCF_030408675.1_ASM3040867v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408675.1_ASM3040867v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:55,388] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:55,413] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:55,413] [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_013410305.1	s__Corynebacterium durum	99.9992	928	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.07	97.26	0.97	0.94	4	conclusive
GCF_000590555.1	s__Corynebacterium argentoratense	78.7989	113	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.97	98.97	0.98	0.98	3	-
GCF_001941445.1	s__Corynebacterium aquilae	78.6881	141	928	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	78.4646	138	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_009734385.1	s__Corynebacterium sp009734385	78.4021	107	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	78.3557	90	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734425.1	s__Corynebacterium sp009734425	78.2789	119	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011325.1	s__Corynebacterium glutamicum	78.1651	88	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.67	97.34	0.92	0.85	76	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.1107	118	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019209935.1	s__Corynebacterium sp019209935	78.0785	103	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.84	95.84	0.96	0.96	2	-
GCA_014490595.1	s__Corynebacterium sp014490595	77.9687	68	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.54	97.13	0.94	0.90	3	-
GCF_900105305.1	s__Corynebacterium timonense	77.852	83	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCF_016595275.1	s__Corynebacterium sp016595275	77.7783	125	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859215.1	s__Corynebacterium canis	77.7633	146	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004382825.2	s__Corynebacterium silvaticum	77.6827	73	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.94	99.78	1.00	0.99	8	-
GCF_900113445.1	s__Corynebacterium spheniscorum	77.5469	95	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_016342275.1	s__Corynebacterium sp016342275	77.5192	111	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103625.1	s__Corynebacterium mycetoides	77.404	94	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372385.1	s__Corynebacterium ciconiae	77.3544	118	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003955685.1	s__Corynebacterium sp003955685	77.2449	114	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001806875.1	s__Corynebacterium sp001806875	77.1724	68	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006334925.1	s__Corynebacterium tapiri	77.1133	84	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339505.1	s__Corynebacterium sp002339505	76.9292	75	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807265.1	s__Corynebacterium sp001807265	76.4952	84	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:55,415] [INFO] GTDB search result was written to GCF_030408675.1_ASM3040867v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:55,416] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:55,420] [INFO] DFAST_QC result json was written to GCF_030408675.1_ASM3040867v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:55,421] [INFO] DFAST_QC completed!
[2024-01-24 11:21:55,421] [INFO] Total running time: 0h1m5s