[2024-01-24 13:18:30,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:30,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:30,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg1505b8c6-2f5a-4c86-aa45-f98d39d44a75/dqc_reference
[2024-01-24 13:18:31,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:31,567] [INFO] Task started: Prodigal
[2024-01-24 13:18:31,568] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc684718-0e61-4962-9121-3dbdf3a08cb5/GCF_031822395.1_ASM3182239v1_genomic.fna.gz | prodigal -d GCF_031822395.1_ASM3182239v1_genomic.fna/cds.fna -a GCF_031822395.1_ASM3182239v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:38,732] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:38,732] [INFO] Task started: HMMsearch
[2024-01-24 13:18:38,732] [INFO] Running command: hmmsearch --tblout GCF_031822395.1_ASM3182239v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1505b8c6-2f5a-4c86-aa45-f98d39d44a75/dqc_reference/reference_markers.hmm GCF_031822395.1_ASM3182239v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:39,042] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:39,043] [INFO] Found 6/6 markers.
[2024-01-24 13:18:39,071] [INFO] Query marker FASTA was written to GCF_031822395.1_ASM3182239v1_genomic.fna/markers.fasta
[2024-01-24 13:18:39,072] [INFO] Task started: Blastn
[2024-01-24 13:18:39,072] [INFO] Running command: blastn -query GCF_031822395.1_ASM3182239v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1505b8c6-2f5a-4c86-aa45-f98d39d44a75/dqc_reference/reference_markers.fasta -out GCF_031822395.1_ASM3182239v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:39,711] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:39,715] [INFO] Selected 30 target genomes.
[2024-01-24 13:18:39,715] [INFO] Target genome list was writen to GCF_031822395.1_ASM3182239v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:39,739] [INFO] Task started: fastANI
[2024-01-24 13:18:39,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc684718-0e61-4962-9121-3dbdf3a08cb5/GCF_031822395.1_ASM3182239v1_genomic.fna.gz --refList GCF_031822395.1_ASM3182239v1_genomic.fna/target_genomes.txt --output GCF_031822395.1_ASM3182239v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:57,166] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:57,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1505b8c6-2f5a-4c86-aa45-f98d39d44a75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:57,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1505b8c6-2f5a-4c86-aa45-f98d39d44a75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:57,176] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:57,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:57,176] [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
Sporosarcina pasteurii	strain=NCTC4822	GCA_900457495.1	1474	1474	type	True	99.9959	1074	1075	95	conclusive
Sporosarcina ureilytica	strain=LMG 22257	GCA_001753205.1	298596	298596	type	True	89.9357	866	1075	95	below_threshold
Sporosarcina jiandibaonis	strain=LAM9210	GCA_013184495.1	2715535	2715535	type	True	77.8629	241	1075	95	below_threshold
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	77.063	72	1075	95	below_threshold
Filibacter tadaridae		GCA_900609045.1	2483811	2483811	type	True	76.993	112	1075	95	below_threshold
Sporosarcina limicola	strain=DSM 13886	GCA_014873855.1	34101	34101	type	True	76.9573	109	1075	95	below_threshold
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	76.4329	81	1075	95	below_threshold
Psychrobacillus lasiicapitis	strain=CGMCC 1.15308	GCA_014641675.1	1636719	1636719	type	True	76.3698	84	1075	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	76.1294	76	1075	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	75.8023	53	1075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:57,178] [INFO] DFAST Taxonomy check result was written to GCF_031822395.1_ASM3182239v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:57,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:57,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:57,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1505b8c6-2f5a-4c86-aa45-f98d39d44a75/dqc_reference/checkm_data
[2024-01-24 13:18:57,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:57,223] [INFO] Task started: CheckM
[2024-01-24 13:18:57,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031822395.1_ASM3182239v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031822395.1_ASM3182239v1_genomic.fna/checkm_input GCF_031822395.1_ASM3182239v1_genomic.fna/checkm_result
[2024-01-24 13:19:25,703] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:25,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:25,737] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:25,738] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:25,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031822395.1_ASM3182239v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:25,739] [INFO] Task started: Blastn
[2024-01-24 13:19:25,739] [INFO] Running command: blastn -query GCF_031822395.1_ASM3182239v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1505b8c6-2f5a-4c86-aa45-f98d39d44a75/dqc_reference/reference_markers_gtdb.fasta -out GCF_031822395.1_ASM3182239v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:26,591] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:26,595] [INFO] Selected 22 target genomes.
[2024-01-24 13:19:26,595] [INFO] Target genome list was writen to GCF_031822395.1_ASM3182239v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:26,617] [INFO] Task started: fastANI
[2024-01-24 13:19:26,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc684718-0e61-4962-9121-3dbdf3a08cb5/GCF_031822395.1_ASM3182239v1_genomic.fna.gz --refList GCF_031822395.1_ASM3182239v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031822395.1_ASM3182239v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:40,532] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:40,545] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:40,546] [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_900457495.1	s__Sporosarcina pasteurii	99.9959	1074	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001753205.1	s__Sporosarcina ureilytica	89.9531	865	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184495.1	s__Sporosarcina sp013184495	77.8432	243	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017921835.1	s__Sporosarcina sp017921835	77.7725	218	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001563475.1	s__Sporosarcina sp001563475	77.3746	146	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018140925.1	s__Psychrobacillus sp018140925	77.2851	63	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014282005.1	s__Sporosarcina sp014282005	77.2355	125	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	96.23	96.23	0.81	0.81	2	-
GCF_017347095.1	s__Sporosarcina sp017347095	77.1176	115	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861775.1	s__Psychrobacillus soli	77.063	72	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900609045.1	s__Sporosarcina tadaridae	77.0165	111	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873855.1	s__Sporosarcina limicola	76.9573	109	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861795.1	s__Psychrobacillus lasiicapitis	76.4329	81	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900111345.1	s__Psychrobacillus sp900111345	76.4221	85	1075	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:40,552] [INFO] GTDB search result was written to GCF_031822395.1_ASM3182239v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:40,552] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:40,556] [INFO] DFAST_QC result json was written to GCF_031822395.1_ASM3182239v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:40,556] [INFO] DFAST_QC completed!
[2024-01-24 13:19:40,557] [INFO] Total running time: 0h1m10s