[2024-01-24 12:21:44,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,173] [INFO] DQC Reference Directory: /var/lib/cwl/stged220453-5fd4-47ae-888a-b26319e64468/dqc_reference
[2024-01-24 12:21:45,515] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,515] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,516] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8d27044-c806-42dc-a2eb-1aa7d9a05c4c/GCF_022968795.1_ASM2296879v1_genomic.fna.gz | prodigal -d GCF_022968795.1_ASM2296879v1_genomic.fna/cds.fna -a GCF_022968795.1_ASM2296879v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:04,228] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:04,229] [INFO] Task started: HMMsearch
[2024-01-24 12:22:04,229] [INFO] Running command: hmmsearch --tblout GCF_022968795.1_ASM2296879v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged220453-5fd4-47ae-888a-b26319e64468/dqc_reference/reference_markers.hmm GCF_022968795.1_ASM2296879v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:04,633] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:04,634] [INFO] Found 6/6 markers.
[2024-01-24 12:22:04,734] [INFO] Query marker FASTA was written to GCF_022968795.1_ASM2296879v1_genomic.fna/markers.fasta
[2024-01-24 12:22:04,735] [INFO] Task started: Blastn
[2024-01-24 12:22:04,735] [INFO] Running command: blastn -query GCF_022968795.1_ASM2296879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged220453-5fd4-47ae-888a-b26319e64468/dqc_reference/reference_markers.fasta -out GCF_022968795.1_ASM2296879v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:05,510] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:05,517] [INFO] Selected 28 target genomes.
[2024-01-24 12:22:05,517] [INFO] Target genome list was writen to GCF_022968795.1_ASM2296879v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:05,543] [INFO] Task started: fastANI
[2024-01-24 12:22:05,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8d27044-c806-42dc-a2eb-1aa7d9a05c4c/GCF_022968795.1_ASM2296879v1_genomic.fna.gz --refList GCF_022968795.1_ASM2296879v1_genomic.fna/target_genomes.txt --output GCF_022968795.1_ASM2296879v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:26,295] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:26,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged220453-5fd4-47ae-888a-b26319e64468/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:26,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged220453-5fd4-47ae-888a-b26319e64468/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:26,313] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:26,314] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:26,314] [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
Desulfatitalea tepidiphila	strain=S28bF	GCA_001293685.1	1185843	1185843	type	True	78.0429	474	1651	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_001854245.1	897	897	type	True	77.1965	134	1651	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_900167235.1	897	897	type	True	77.1332	131	1651	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_002009335.2	897	897	type	True	77.1317	131	1651	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_000422185.1	897	897	type	True	77.0338	127	1651	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	76.9741	240	1651	95	below_threshold
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	76.9656	215	1651	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	76.9532	214	1651	95	below_threshold
Desulfosarcina cetonica	strain=JCM 12296	GCA_001311845.1	90730	90730	type	True	76.8139	207	1651	95	below_threshold
Desulfosudis oleivorans	strain=Hxd3	GCA_000018405.1	181663	181663	type	True	76.5709	140	1651	95	below_threshold
Desulfonema ishimotonii	strain=Tokyo 01	GCA_003851005.1	45657	45657	type	True	76.3693	129	1651	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	75.9732	91	1651	95	below_threshold
Geothermobacter ehrlichii	strain=SS015	GCA_008124615.1	213224	213224	type	True	75.8772	66	1651	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.8753	75	1651	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	75.8011	73	1651	95	below_threshold
Desulfofustis glycolicus	strain=DSM 9705	GCA_900130015.1	51195	51195	type	True	75.7658	70	1651	95	below_threshold
Desulfacinum infernum	strain=DSM 9756	GCA_900129305.1	35837	35837	type	True	75.7524	94	1651	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	75.6367	51	1651	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.5571	65	1651	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	75.3862	50	1651	95	below_threshold
Chelatococcus reniformis	strain=CGMCC 1.12919	GCA_014640075.1	1494448	1494448	type	True	75.0977	52	1651	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.0611	52	1651	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:26,316] [INFO] DFAST Taxonomy check result was written to GCF_022968795.1_ASM2296879v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:26,316] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:26,316] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:26,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged220453-5fd4-47ae-888a-b26319e64468/dqc_reference/checkm_data
[2024-01-24 12:22:26,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:26,370] [INFO] Task started: CheckM
[2024-01-24 12:22:26,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022968795.1_ASM2296879v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022968795.1_ASM2296879v1_genomic.fna/checkm_input GCF_022968795.1_ASM2296879v1_genomic.fna/checkm_result
[2024-01-24 12:23:23,580] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:23,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:23,606] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:23,606] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:23,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022968795.1_ASM2296879v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:23,607] [INFO] Task started: Blastn
[2024-01-24 12:23:23,607] [INFO] Running command: blastn -query GCF_022968795.1_ASM2296879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged220453-5fd4-47ae-888a-b26319e64468/dqc_reference/reference_markers_gtdb.fasta -out GCF_022968795.1_ASM2296879v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:24,605] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:24,611] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:24,611] [INFO] Target genome list was writen to GCF_022968795.1_ASM2296879v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:24,707] [INFO] Task started: fastANI
[2024-01-24 12:23:24,707] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8d27044-c806-42dc-a2eb-1aa7d9a05c4c/GCF_022968795.1_ASM2296879v1_genomic.fna.gz --refList GCF_022968795.1_ASM2296879v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022968795.1_ASM2296879v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:41,563] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:41,592] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:23:41,592] [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_018224505.1	s__Desulfatitalea sp018224505	80.8085	632	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218685.1	s__Desulfatitalea sp016218685	78.7134	367	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293685.1	s__Desulfatitalea tepidiphila	78.0318	476	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002402905.1	s__Desulfatitalea sp002402905	77.9955	375	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599575.1	s__Desulfatitalea sp003599575	77.5395	334	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961655.1	s__Desulfatitalea sp000961655	77.4711	313	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041835.1	s__Desulfatitalea sp013041835	77.2506	187	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	99.91	99.91	0.92	0.92	2	-
GCA_011042305.1	s__UBA2174 sp011042305	77.1866	213	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA2174;g__UBA2174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432195.1	s__UBA5852 sp002432195	76.8566	220	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA5852;g__UBA5852	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390065.1	s__JAABTD01 sp011390065	76.5807	189	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018405.1	s__Desulfosudis oleovorans	76.5709	140	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosudaceae;g__Desulfosudis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390035.1	s__JAABTE01 sp011390035	76.5018	132	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390315.1	s__JAABSQ01 sp011390315	76.3784	129	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390345.1	s__JAABSP01 sp011390345	76.3146	136	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABSP01	95.0	95.08	95.08	0.82	0.82	2	-
GCA_002348005.1	s__UBA2230 sp002348005	76.2258	90	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__UBA2230	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342285.1	s__JAEINQ01 sp016342285	76.2057	172	1651	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__JAEINQ01;g__JAEINQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	75.2255	51	1651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:41,594] [INFO] GTDB search result was written to GCF_022968795.1_ASM2296879v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:41,594] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:41,599] [INFO] DFAST_QC result json was written to GCF_022968795.1_ASM2296879v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:41,600] [INFO] DFAST_QC completed!
[2024-01-24 12:23:41,600] [INFO] Total running time: 0h1m57s