[2024-01-24 15:10:33,243] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:33,245] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:33,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg23bdbd1a-5e77-48c7-b752-3e23b8531940/dqc_reference
[2024-01-24 15:10:37,184] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:37,185] [INFO] Task started: Prodigal
[2024-01-24 15:10:37,185] [INFO] Running command: gunzip -c /var/lib/cwl/stgb746a6fd-0a10-418f-ba10-8f16f4b80b4f/GCF_001021065.1_ASM102106v1_genomic.fna.gz | prodigal -d GCF_001021065.1_ASM102106v1_genomic.fna/cds.fna -a GCF_001021065.1_ASM102106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:44,599] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:44,600] [INFO] Task started: HMMsearch
[2024-01-24 15:10:44,600] [INFO] Running command: hmmsearch --tblout GCF_001021065.1_ASM102106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23bdbd1a-5e77-48c7-b752-3e23b8531940/dqc_reference/reference_markers.hmm GCF_001021065.1_ASM102106v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:44,837] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:44,838] [INFO] Found 6/6 markers.
[2024-01-24 15:10:44,866] [INFO] Query marker FASTA was written to GCF_001021065.1_ASM102106v1_genomic.fna/markers.fasta
[2024-01-24 15:10:44,866] [INFO] Task started: Blastn
[2024-01-24 15:10:44,866] [INFO] Running command: blastn -query GCF_001021065.1_ASM102106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23bdbd1a-5e77-48c7-b752-3e23b8531940/dqc_reference/reference_markers.fasta -out GCF_001021065.1_ASM102106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:47,473] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:47,477] [INFO] Selected 19 target genomes.
[2024-01-24 15:10:47,477] [INFO] Target genome list was writen to GCF_001021065.1_ASM102106v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:47,539] [INFO] Task started: fastANI
[2024-01-24 15:10:47,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgb746a6fd-0a10-418f-ba10-8f16f4b80b4f/GCF_001021065.1_ASM102106v1_genomic.fna.gz --refList GCF_001021065.1_ASM102106v1_genomic.fna/target_genomes.txt --output GCF_001021065.1_ASM102106v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:57,258] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:57,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23bdbd1a-5e77-48c7-b752-3e23b8531940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:57,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23bdbd1a-5e77-48c7-b752-3e23b8531940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:57,286] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:57,286] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:57,286] [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 uterequi	strain=DSM 45634	GCA_001021065.1	1072256	1072256	type	True	100.0	805	806	95	conclusive
Corynebacterium doosanense	strain=CAU 212	GCA_000767055.1	1121358	1121358	type	True	79.248	321	806	95	below_threshold
Corynebacterium yudongzhengii	strain=2183	GCA_003065405.1	2080740	2080740	type	True	79.1164	314	806	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	79.0818	268	806	95	below_threshold
Corynebacterium doosanense	strain=DSM 45436	GCA_000372245.1	1121358	1121358	type	True	78.924	321	806	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.8926	306	806	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	78.8415	301	806	95	below_threshold
Corynebacterium maris	strain=DSM 45190	GCA_000442645.1	575200	575200	type	True	78.7603	307	806	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	78.7377	302	806	95	below_threshold
Corynebacterium tapiri	strain=LMG 28165	GCA_006334925.1	1448266	1448266	type	True	78.5835	233	806	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.572	291	806	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	78.5396	257	806	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	78.3207	213	806	95	below_threshold
Corynebacterium lipophiloflavum	strain=DSM 44291	GCA_000159635.1	161889	161889	type	True	78.3143	207	806	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	78.2419	226	806	95	below_threshold
Corynebacterium urinipleomorphum	strain=Marseille-P2799	GCA_900155535.1	1852380	1852380	type	True	78.1465	177	806	95	below_threshold
Corynebacterium renale	strain=NCTC7448	GCA_900478035.1	1724	1724	type	True	77.8575	127	806	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	75.6786	128	806	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	75.6512	128	806	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:57,288] [INFO] DFAST Taxonomy check result was written to GCF_001021065.1_ASM102106v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:57,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:57,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:57,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23bdbd1a-5e77-48c7-b752-3e23b8531940/dqc_reference/checkm_data
[2024-01-24 15:10:57,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:57,325] [INFO] Task started: CheckM
[2024-01-24 15:10:57,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001021065.1_ASM102106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001021065.1_ASM102106v1_genomic.fna/checkm_input GCF_001021065.1_ASM102106v1_genomic.fna/checkm_result
[2024-01-24 15:11:26,530] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:26,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:26,552] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:26,552] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:26,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001021065.1_ASM102106v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:26,553] [INFO] Task started: Blastn
[2024-01-24 15:11:26,553] [INFO] Running command: blastn -query GCF_001021065.1_ASM102106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23bdbd1a-5e77-48c7-b752-3e23b8531940/dqc_reference/reference_markers_gtdb.fasta -out GCF_001021065.1_ASM102106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:28,071] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:28,075] [INFO] Selected 19 target genomes.
[2024-01-24 15:11:28,076] [INFO] Target genome list was writen to GCF_001021065.1_ASM102106v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:28,093] [INFO] Task started: fastANI
[2024-01-24 15:11:28,094] [INFO] Running command: fastANI --query /var/lib/cwl/stgb746a6fd-0a10-418f-ba10-8f16f4b80b4f/GCF_001021065.1_ASM102106v1_genomic.fna.gz --refList GCF_001021065.1_ASM102106v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001021065.1_ASM102106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:38,851] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:38,865] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:38,865] [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_001021065.1	s__Corynebacterium uterequi	100.0	805	806	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_000767055.1	s__Corynebacterium doosanense	79.2154	321	806	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	79.1887	300	806	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_003065405.1	s__Corynebacterium yudongzhengii	79.1387	314	806	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900411315.1	s__Corynebacterium senegalense	79.0885	268	806	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	78.8757	305	806	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177745.1	s__Corynebacterium pollutisoli	78.8415	301	806	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_000442645.1	s__Corynebacterium maris	78.7509	308	806	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	78.6002	232	806	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	78.5428	257	806	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577555.1	s__Corynebacterium jeddahense	78.3439	229	806	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159635.1	s__Corynebacterium lipophiloflavum	78.3143	207	806	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	78.2525	240	806	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351335.1	s__Corynebacterium lipophilum	78.2419	226	806	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	78.2308	211	806	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900156035.1	s__Corynebacterium afermentans	78.1588	210	806	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_002563965.1	s__Corynebacterium renale	77.7173	126	806	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.02	98.07	0.97	0.94	5	-
GCF_003427025.1	s__Jiangella endophytica	75.6717	129	806	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:38,867] [INFO] GTDB search result was written to GCF_001021065.1_ASM102106v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:38,867] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:38,871] [INFO] DFAST_QC result json was written to GCF_001021065.1_ASM102106v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:38,871] [INFO] DFAST_QC completed!
[2024-01-24 15:11:38,872] [INFO] Total running time: 0h1m6s