[2024-01-24 11:35:24,380] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:24,401] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:24,402] [INFO] DQC Reference Directory: /var/lib/cwl/stgb019ade3-eaf8-4856-93e6-fb79dbaf03be/dqc_reference
[2024-01-24 11:35:26,507] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,508] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,508] [INFO] Running command: gunzip -c /var/lib/cwl/stga1c908df-fbe0-4040-a842-deefc9f82100/GCF_016595285.2_ASM1659528v2_genomic.fna.gz | prodigal -d GCF_016595285.2_ASM1659528v2_genomic.fna/cds.fna -a GCF_016595285.2_ASM1659528v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:34,171] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:34,171] [INFO] Task started: HMMsearch
[2024-01-24 11:35:34,172] [INFO] Running command: hmmsearch --tblout GCF_016595285.2_ASM1659528v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb019ade3-eaf8-4856-93e6-fb79dbaf03be/dqc_reference/reference_markers.hmm GCF_016595285.2_ASM1659528v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:34,468] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:34,470] [INFO] Found 6/6 markers.
[2024-01-24 11:35:34,494] [INFO] Query marker FASTA was written to GCF_016595285.2_ASM1659528v2_genomic.fna/markers.fasta
[2024-01-24 11:35:34,495] [INFO] Task started: Blastn
[2024-01-24 11:35:34,495] [INFO] Running command: blastn -query GCF_016595285.2_ASM1659528v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb019ade3-eaf8-4856-93e6-fb79dbaf03be/dqc_reference/reference_markers.fasta -out GCF_016595285.2_ASM1659528v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:35,527] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:35,530] [INFO] Selected 16 target genomes.
[2024-01-24 11:35:35,531] [INFO] Target genome list was writen to GCF_016595285.2_ASM1659528v2_genomic.fna/target_genomes.txt
[2024-01-24 11:35:35,537] [INFO] Task started: fastANI
[2024-01-24 11:35:35,537] [INFO] Running command: fastANI --query /var/lib/cwl/stga1c908df-fbe0-4040-a842-deefc9f82100/GCF_016595285.2_ASM1659528v2_genomic.fna.gz --refList GCF_016595285.2_ASM1659528v2_genomic.fna/target_genomes.txt --output GCF_016595285.2_ASM1659528v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:43,548] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:43,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb019ade3-eaf8-4856-93e6-fb79dbaf03be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:43,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb019ade3-eaf8-4856-93e6-fb79dbaf03be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:43,568] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:43,568] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:43,568] [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 halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	79.2497	331	856	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	79.2325	323	856	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	79.055	324	856	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.9522	293	856	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	78.9378	330	856	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	78.9324	322	856	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	78.9181	299	856	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_000183325.2	36808	36808	type	True	78.8223	208	856	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.7078	212	856	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	78.6444	300	856	95	below_threshold
Corynebacterium variabile	strain=NBRC 15286	GCA_006539825.1	1727	1727	type	True	78.6161	235	856	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_014191555.1	36808	36808	type	True	78.5706	241	856	95	below_threshold
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	78.5323	245	856	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000011305.1	152794	152794	type	True	78.3306	252	856	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000160795.1	152794	152794	type	True	78.2607	260	856	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	76.5914	149	856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:43,570] [INFO] DFAST Taxonomy check result was written to GCF_016595285.2_ASM1659528v2_genomic.fna/tc_result.tsv
[2024-01-24 11:35:43,571] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:43,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:43,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb019ade3-eaf8-4856-93e6-fb79dbaf03be/dqc_reference/checkm_data
[2024-01-24 11:35:43,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:43,599] [INFO] Task started: CheckM
[2024-01-24 11:35:43,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016595285.2_ASM1659528v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016595285.2_ASM1659528v2_genomic.fna/checkm_input GCF_016595285.2_ASM1659528v2_genomic.fna/checkm_result
[2024-01-24 11:36:12,240] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:12,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:12,262] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:12,262] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:12,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016595285.2_ASM1659528v2_genomic.fna/markers.fasta)
[2024-01-24 11:36:12,263] [INFO] Task started: Blastn
[2024-01-24 11:36:12,263] [INFO] Running command: blastn -query GCF_016595285.2_ASM1659528v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb019ade3-eaf8-4856-93e6-fb79dbaf03be/dqc_reference/reference_markers_gtdb.fasta -out GCF_016595285.2_ASM1659528v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:13,735] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:13,739] [INFO] Selected 9 target genomes.
[2024-01-24 11:36:13,739] [INFO] Target genome list was writen to GCF_016595285.2_ASM1659528v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:13,757] [INFO] Task started: fastANI
[2024-01-24 11:36:13,757] [INFO] Running command: fastANI --query /var/lib/cwl/stga1c908df-fbe0-4040-a842-deefc9f82100/GCF_016595285.2_ASM1659528v2_genomic.fna.gz --refList GCF_016595285.2_ASM1659528v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016595285.2_ASM1659528v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:19,154] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:19,163] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:19,163] [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
GCA_019209935.1	s__Corynebacterium sp019209935	95.7833	818	856	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.84	95.84	0.96	0.96	2	conclusive
GCF_016342265.1	s__Corynebacterium sp016342265	90.9747	788	856	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016342275.1	s__Corynebacterium sp016342275	87.5143	771	856	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	86.7357	714	856	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	79.2497	331	856	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000819445.1	s__Corynebacterium humireducens	79.0693	323	856	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_002994655.1	s__Corynebacterium sp002994655	79.0536	271	856	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	78.4232	275	856	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	78.3306	252	856	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:19,165] [INFO] GTDB search result was written to GCF_016595285.2_ASM1659528v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:19,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:19,170] [INFO] DFAST_QC result json was written to GCF_016595285.2_ASM1659528v2_genomic.fna/dqc_result.json
[2024-01-24 11:36:19,171] [INFO] DFAST_QC completed!
[2024-01-24 11:36:19,171] [INFO] Total running time: 0h0m55s