[2024-01-24 14:06:04,407] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:04,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:04,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg592de016-b2c8-4577-9181-eafb70c9717e/dqc_reference
[2024-01-24 14:06:05,635] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:05,637] [INFO] Task started: Prodigal
[2024-01-24 14:06:05,637] [INFO] Running command: gunzip -c /var/lib/cwl/stg19fabe14-e981-44a8-85a4-b542a9d904b0/GCF_013410305.1_ASM1341030v1_genomic.fna.gz | prodigal -d GCF_013410305.1_ASM1341030v1_genomic.fna/cds.fna -a GCF_013410305.1_ASM1341030v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:17,813] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:17,814] [INFO] Task started: HMMsearch
[2024-01-24 14:06:17,814] [INFO] Running command: hmmsearch --tblout GCF_013410305.1_ASM1341030v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg592de016-b2c8-4577-9181-eafb70c9717e/dqc_reference/reference_markers.hmm GCF_013410305.1_ASM1341030v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:18,097] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:18,098] [INFO] Found 6/6 markers.
[2024-01-24 14:06:18,124] [INFO] Query marker FASTA was written to GCF_013410305.1_ASM1341030v1_genomic.fna/markers.fasta
[2024-01-24 14:06:18,124] [INFO] Task started: Blastn
[2024-01-24 14:06:18,124] [INFO] Running command: blastn -query GCF_013410305.1_ASM1341030v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg592de016-b2c8-4577-9181-eafb70c9717e/dqc_reference/reference_markers.fasta -out GCF_013410305.1_ASM1341030v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:19,013] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:19,017] [INFO] Selected 23 target genomes.
[2024-01-24 14:06:19,017] [INFO] Target genome list was writen to GCF_013410305.1_ASM1341030v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:19,029] [INFO] Task started: fastANI
[2024-01-24 14:06:19,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg19fabe14-e981-44a8-85a4-b542a9d904b0/GCF_013410305.1_ASM1341030v1_genomic.fna.gz --refList GCF_013410305.1_ASM1341030v1_genomic.fna/target_genomes.txt --output GCF_013410305.1_ASM1341030v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:29,669] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:29,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg592de016-b2c8-4577-9181-eafb70c9717e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:29,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg592de016-b2c8-4577-9181-eafb70c9717e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:29,688] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:29,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:29,689] [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	100.0	932	933	95	conclusive
Corynebacterium argentoratense	strain=DSM 44202	GCA_000590555.1	42817	42817	type	True	78.9925	126	933	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.8334	134	933	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.7053	146	933	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_000011325.1	1718	1718	type	True	78.5953	92	933	95	below_threshold
Corynebacterium kalinowskii	strain=1959	GCA_009734385.1	2675216	2675216	type	True	78.5557	102	933	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	78.4607	112	933	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032 substr. K051	GCA_000382905.1	1718	1718	type	True	78.4346	91	933	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_002847405.1	1718	1718	type	True	78.2802	91	933	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.0043	118	933	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	77.9199	124	933	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	77.8583	84	933	95	below_threshold
Corynebacterium canis	strain=CCUG 58627	GCA_007859215.1	679663	679663	type	True	77.733	151	933	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	77.5772	92	933	95	below_threshold
Corynebacterium ciconiae	strain=DSM 44920	GCA_000372385.1	227319	227319	type	True	77.544	114	933	95	below_threshold
Corynebacterium silvaticum	strain=KL0182	GCA_004382825.2	2320431	2320431	type	True	77.5174	75	933	95	below_threshold
Corynebacterium timonense	strain=DSM 45434	GCA_900105305.1	441500	441500	type	True	77.4384	82	933	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	77.2839	109	933	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	77.2533	72	933	95	below_threshold
Corynebacterium tapiri	strain=LMG 28165	GCA_006334925.1	1448266	1448266	type	True	77.2097	74	933	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	77.2003	114	933	95	below_threshold
Corynebacterium wankanglinii	strain=zg-913	GCA_013601005.1	2735136	2735136	type	True	77.0429	71	933	95	below_threshold
Corynebacterium timonense	strain=5401744	GCA_000312345.1	441500	441500	type	True	77.021	80	933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:29,690] [INFO] DFAST Taxonomy check result was written to GCF_013410305.1_ASM1341030v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:29,691] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:29,691] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:29,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg592de016-b2c8-4577-9181-eafb70c9717e/dqc_reference/checkm_data
[2024-01-24 14:06:29,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:29,727] [INFO] Task started: CheckM
[2024-01-24 14:06:29,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013410305.1_ASM1341030v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013410305.1_ASM1341030v1_genomic.fna/checkm_input GCF_013410305.1_ASM1341030v1_genomic.fna/checkm_result
[2024-01-24 14:07:07,535] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:07,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:07,557] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:07,557] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:07,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013410305.1_ASM1341030v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:07,558] [INFO] Task started: Blastn
[2024-01-24 14:07:07,558] [INFO] Running command: blastn -query GCF_013410305.1_ASM1341030v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg592de016-b2c8-4577-9181-eafb70c9717e/dqc_reference/reference_markers_gtdb.fasta -out GCF_013410305.1_ASM1341030v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:08,796] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:08,801] [INFO] Selected 24 target genomes.
[2024-01-24 14:07:08,802] [INFO] Target genome list was writen to GCF_013410305.1_ASM1341030v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:08,816] [INFO] Task started: fastANI
[2024-01-24 14:07:08,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg19fabe14-e981-44a8-85a4-b542a9d904b0/GCF_013410305.1_ASM1341030v1_genomic.fna.gz --refList GCF_013410305.1_ASM1341030v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013410305.1_ASM1341030v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:19,125] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:19,148] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:19,148] [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	100.0	932	933	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_000550805.1	s__Corynebacterium vitaeruminis	78.9428	135	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_000590555.1	s__Corynebacterium argentoratense	78.7594	124	933	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	78.7386	148	933	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	78.6229	92	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.67	97.34	0.92	0.85	76	-
GCA_014490595.1	s__Corynebacterium sp014490595	78.4716	66	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.54	97.13	0.94	0.90	3	-
GCF_009734385.1	s__Corynebacterium sp009734385	78.4642	101	933	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	78.3434	113	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.1159	119	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	78.036	85	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595275.1	s__Corynebacterium sp016595275	77.8827	121	933	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	77.8308	94	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019209935.1	s__Corynebacterium sp019209935	77.7552	104	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.84	95.84	0.96	0.96	2	-
GCF_016342275.1	s__Corynebacterium sp016342275	77.7489	105	933	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	77.733	151	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105305.1	s__Corynebacterium timonense	77.5882	83	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000372385.1	s__Corynebacterium ciconiae	77.544	114	933	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	77.5174	75	933	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	77.4821	93	933	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003955685.1	s__Corynebacterium sp003955685	77.4626	106	933	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	77.2166	64	933	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	77.2097	74	933	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	76.9473	77	933	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	76.478	90	933	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 14:07:19,150] [INFO] GTDB search result was written to GCF_013410305.1_ASM1341030v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:19,150] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:19,155] [INFO] DFAST_QC result json was written to GCF_013410305.1_ASM1341030v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:19,155] [INFO] DFAST_QC completed!
[2024-01-24 14:07:19,155] [INFO] Total running time: 0h1m15s