[2024-01-24 13:02:03,905] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:03,909] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:03,909] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d67c314-46a0-4d8f-a61e-e61715bdb99b/dqc_reference
[2024-01-24 13:02:05,225] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:05,226] [INFO] Task started: Prodigal
[2024-01-24 13:02:05,226] [INFO] Running command: gunzip -c /var/lib/cwl/stg525b5bdc-9fc7-4a5f-b981-c9ae7e234b96/GCF_001941445.1_ASM194144v1_genomic.fna.gz | prodigal -d GCF_001941445.1_ASM194144v1_genomic.fna/cds.fna -a GCF_001941445.1_ASM194144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:15,473] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:15,473] [INFO] Task started: HMMsearch
[2024-01-24 13:02:15,473] [INFO] Running command: hmmsearch --tblout GCF_001941445.1_ASM194144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d67c314-46a0-4d8f-a61e-e61715bdb99b/dqc_reference/reference_markers.hmm GCF_001941445.1_ASM194144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:15,673] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:15,676] [INFO] Found 6/6 markers.
[2024-01-24 13:02:15,700] [INFO] Query marker FASTA was written to GCF_001941445.1_ASM194144v1_genomic.fna/markers.fasta
[2024-01-24 13:02:15,700] [INFO] Task started: Blastn
[2024-01-24 13:02:15,700] [INFO] Running command: blastn -query GCF_001941445.1_ASM194144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d67c314-46a0-4d8f-a61e-e61715bdb99b/dqc_reference/reference_markers.fasta -out GCF_001941445.1_ASM194144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:16,638] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:16,642] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:16,643] [INFO] Target genome list was writen to GCF_001941445.1_ASM194144v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:16,649] [INFO] Task started: fastANI
[2024-01-24 13:02:16,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg525b5bdc-9fc7-4a5f-b981-c9ae7e234b96/GCF_001941445.1_ASM194144v1_genomic.fna.gz --refList GCF_001941445.1_ASM194144v1_genomic.fna/target_genomes.txt --output GCF_001941445.1_ASM194144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:24,264] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:24,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d67c314-46a0-4d8f-a61e-e61715bdb99b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:24,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d67c314-46a0-4d8f-a61e-e61715bdb99b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:24,277] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:24,277] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:24,277] [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 aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	100.0	975	975	95	conclusive
Corynebacterium argentoratense	strain=DSM 44202	GCA_000590555.1	42817	42817	type	True	79.9789	207	975	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	79.6426	246	975	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	79.1346	212	975	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	79.1292	244	975	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.9285	243	975	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000011305.1	152794	152794	type	True	78.8815	195	975	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	78.873	235	975	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	78.8354	195	975	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.8188	239	975	95	below_threshold
Corynebacterium maris	strain=DSM 45190	GCA_000442645.1	575200	575200	type	True	78.7281	184	975	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	78.7012	231	975	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000160795.1	152794	152794	type	True	78.4687	188	975	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	78.3019	137	975	95	below_threshold
Corynebacterium ureicelerivorans	strain=IMMIB RIV-2301	GCA_000747315.1	401472	401472	type	True	78.2442	130	975	95	below_threshold
Corynebacterium spheniscorum	strain=CCUG 45512	GCA_008693095.1	185761	185761	type	True	78.1781	141	975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:24,279] [INFO] DFAST Taxonomy check result was written to GCF_001941445.1_ASM194144v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:24,280] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:24,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:24,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d67c314-46a0-4d8f-a61e-e61715bdb99b/dqc_reference/checkm_data
[2024-01-24 13:02:24,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:24,309] [INFO] Task started: CheckM
[2024-01-24 13:02:24,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001941445.1_ASM194144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001941445.1_ASM194144v1_genomic.fna/checkm_input GCF_001941445.1_ASM194144v1_genomic.fna/checkm_result
[2024-01-24 13:02:56,933] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:56,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:56,956] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:56,956] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:56,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001941445.1_ASM194144v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:56,957] [INFO] Task started: Blastn
[2024-01-24 13:02:56,957] [INFO] Running command: blastn -query GCF_001941445.1_ASM194144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d67c314-46a0-4d8f-a61e-e61715bdb99b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001941445.1_ASM194144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:58,331] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:58,334] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:58,335] [INFO] Target genome list was writen to GCF_001941445.1_ASM194144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:58,343] [INFO] Task started: fastANI
[2024-01-24 13:02:58,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg525b5bdc-9fc7-4a5f-b981-c9ae7e234b96/GCF_001941445.1_ASM194144v1_genomic.fna.gz --refList GCF_001941445.1_ASM194144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001941445.1_ASM194144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:06,370] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:06,383] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:06,383] [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_001941445.1	s__Corynebacterium aquilae	100.0	975	975	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_002994655.1	s__Corynebacterium sp002994655	80.7731	473	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590555.1	s__Corynebacterium argentoratense	80.0344	208	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.97	98.97	0.98	0.98	3	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	79.6426	246	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_000341345.1	s__Corynebacterium halotolerans	79.138	245	975	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	79.028	209	975	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	78.9947	196	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177745.1	s__Corynebacterium pollutisoli	78.873	235	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCA_019209935.1	s__Corynebacterium sp019209935	78.8158	199	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.84	95.84	0.96	0.96	2	-
GCF_000442645.1	s__Corynebacterium maris	78.7484	185	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011305.1	s__Corynebacterium efficiens	78.7331	193	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_009734425.1	s__Corynebacterium sp009734425	78.7015	193	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113445.1	s__Corynebacterium spheniscorum	78.2765	140	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCA_012838985.1	s__Corynebacterium sp012838985	78.0909	189	975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114135.1	s__Corynebacterium avicola	77.8887	164	975	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	77.8783	170	975	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 13:03:06,385] [INFO] GTDB search result was written to GCF_001941445.1_ASM194144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:06,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:06,389] [INFO] DFAST_QC result json was written to GCF_001941445.1_ASM194144v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:06,389] [INFO] DFAST_QC completed!
[2024-01-24 13:03:06,389] [INFO] Total running time: 0h1m2s