[2024-01-24 11:12:56,673] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:56,676] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:56,676] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c3ba6bd-2618-4610-a8c2-2f5d2b7cf495/dqc_reference
[2024-01-24 11:12:58,011] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:58,012] [INFO] Task started: Prodigal
[2024-01-24 11:12:58,012] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbe425d4-3a19-4522-8436-d37ed00a301b/GCF_018494085.1_ASM1849408v1_genomic.fna.gz | prodigal -d GCF_018494085.1_ASM1849408v1_genomic.fna/cds.fna -a GCF_018494085.1_ASM1849408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:05,482] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:05,483] [INFO] Task started: HMMsearch
[2024-01-24 11:13:05,483] [INFO] Running command: hmmsearch --tblout GCF_018494085.1_ASM1849408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c3ba6bd-2618-4610-a8c2-2f5d2b7cf495/dqc_reference/reference_markers.hmm GCF_018494085.1_ASM1849408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:05,754] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:05,756] [INFO] Found 6/6 markers.
[2024-01-24 11:13:05,784] [INFO] Query marker FASTA was written to GCF_018494085.1_ASM1849408v1_genomic.fna/markers.fasta
[2024-01-24 11:13:05,784] [INFO] Task started: Blastn
[2024-01-24 11:13:05,785] [INFO] Running command: blastn -query GCF_018494085.1_ASM1849408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c3ba6bd-2618-4610-a8c2-2f5d2b7cf495/dqc_reference/reference_markers.fasta -out GCF_018494085.1_ASM1849408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:06,591] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:06,611] [INFO] Selected 18 target genomes.
[2024-01-24 11:13:06,611] [INFO] Target genome list was writen to GCF_018494085.1_ASM1849408v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:06,624] [INFO] Task started: fastANI
[2024-01-24 11:13:06,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbe425d4-3a19-4522-8436-d37ed00a301b/GCF_018494085.1_ASM1849408v1_genomic.fna.gz --refList GCF_018494085.1_ASM1849408v1_genomic.fna/target_genomes.txt --output GCF_018494085.1_ASM1849408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:19,877] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:19,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c3ba6bd-2618-4610-a8c2-2f5d2b7cf495/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:19,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c3ba6bd-2618-4610-a8c2-2f5d2b7cf495/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:19,891] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:19,891] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:19,891] [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
Rosenbergiella collisarenosi	strain=8.8A	GCA_018494085.1	1544695	1544695	type	True	100.0	1102	1103	95	conclusive
Rosenbergiella nectarea	strain=8N4	GCA_900111105.1	988801	988801	type	True	82.7361	631	1103	95	below_threshold
Rosenbergiella epipactidis	strain=2.1A	GCA_018494055.1	1544694	1544694	type	True	82.3446	637	1103	95	below_threshold
Rosenbergiella australiborealis	strain=CdVSA20.1	GCA_018494035.1	1544696	1544696	type	True	81.8459	525	1103	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	78.4762	148	1103	95	below_threshold
Tatumella ptyseos	strain=ATCC 33301	GCA_000439895.1	82987	82987	type	True	78.3706	171	1103	95	below_threshold
Erwinia persicina	strain=NBRC 102418	GCA_001571305.1	55211	55211	type	True	78.3498	107	1103	95	below_threshold
Salmonella enterica subsp. houtenae	strain=CCUG 30041T	GCA_008692755.1	59205	28901	type	True	78.328	96	1103	95	below_threshold
Kluyvera intermedia	strain=NBRC 102594	GCA_001598315.1	61648	61648	suspected-type	True	78.02	95	1103	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	77.998	128	1103	95	below_threshold
Yersinia ruckeri	strain=ATCC 29473	GCA_000754815.1	29486	29486	type	True	77.9578	92	1103	95	below_threshold
Yersinia ruckeri	strain=NCTC12986	GCA_900460715.1	29486	29486	type	True	77.9337	92	1103	95	below_threshold
Leminorella grimontii	strain=JCM 5902	GCA_024343555.1	82981	82981	type	True	77.918	51	1103	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	77.8632	94	1103	95	below_threshold
Yersinia ruckeri	strain=ATCC 29473	GCA_000173755.1	29486	29486	type	True	77.7358	84	1103	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	77.7109	65	1103	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:19,894] [INFO] DFAST Taxonomy check result was written to GCF_018494085.1_ASM1849408v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:19,894] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:19,894] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:19,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c3ba6bd-2618-4610-a8c2-2f5d2b7cf495/dqc_reference/checkm_data
[2024-01-24 11:13:19,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:19,930] [INFO] Task started: CheckM
[2024-01-24 11:13:19,930] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018494085.1_ASM1849408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018494085.1_ASM1849408v1_genomic.fna/checkm_input GCF_018494085.1_ASM1849408v1_genomic.fna/checkm_result
[2024-01-24 11:13:48,346] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:48,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:48,366] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:48,366] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:48,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018494085.1_ASM1849408v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:48,367] [INFO] Task started: Blastn
[2024-01-24 11:13:48,368] [INFO] Running command: blastn -query GCF_018494085.1_ASM1849408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c3ba6bd-2618-4610-a8c2-2f5d2b7cf495/dqc_reference/reference_markers_gtdb.fasta -out GCF_018494085.1_ASM1849408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:49,321] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:49,324] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:49,324] [INFO] Target genome list was writen to GCF_018494085.1_ASM1849408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:49,337] [INFO] Task started: fastANI
[2024-01-24 11:13:49,338] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbe425d4-3a19-4522-8436-d37ed00a301b/GCF_018494085.1_ASM1849408v1_genomic.fna.gz --refList GCF_018494085.1_ASM1849408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018494085.1_ASM1849408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:00,700] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:00,713] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:00,713] [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_018494085.1	s__Rosenbergiella collisarenosi	100.0	1102	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	99.00	99.00	0.87	0.87	2	conclusive
GCF_900111105.1	s__Rosenbergiella nectarea	82.731	631	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.23	96.23	0.89	0.89	2	-
GCF_018494055.1	s__Rosenbergiella epipactidis	82.3421	637	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.28	95.56	0.88	0.85	5	-
GCF_018494065.1	s__Rosenbergiella sp018494065	81.9415	627	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018494035.1	s__Rosenbergiella australiborealis	81.8654	523	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290365.1	s__Leclercia sp003024485	78.7829	89	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.06	98.06	0.90	0.90	2	-
GCF_009765445.1	s__Erwinia sp009765445	78.4799	121	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900215435.1	s__Pantoea sp900215435	78.4678	135	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.51	99.02	0.98	0.96	3	-
GCF_001922585.1	s__1-19 sp001922585	78.4522	97	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__1-19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735525.1	s__Tatumella ptyseos	78.4514	168	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	99.71	99.17	0.96	0.91	4	-
GCF_018842675.1	s__Pantoea sp018842675	78.334	139	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101395.1	s__Mixta alhagi	78.2618	128	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018842655.1	s__Pantoea sp018842655	78.1622	130	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002895925.1	s__Mixta theicola	78.1133	127	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007570865.1	s__Atlantibacter subterranea	78.0326	86	1103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.55	98.44	0.93	0.91	8	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:00,716] [INFO] GTDB search result was written to GCF_018494085.1_ASM1849408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:00,716] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:00,720] [INFO] DFAST_QC result json was written to GCF_018494085.1_ASM1849408v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:00,720] [INFO] DFAST_QC completed!
[2024-01-24 11:14:00,721] [INFO] Total running time: 0h1m4s