[2024-01-25 20:28:05,738] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:28:05,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:28:05,740] [INFO] DQC Reference Directory: /var/lib/cwl/stge9c5a909-e11f-425d-a3b8-e14182510ecd/dqc_reference
[2024-01-25 20:28:06,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:28:06,898] [INFO] Task started: Prodigal
[2024-01-25 20:28:06,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg6500c039-2568-4937-8688-9d46e5580930/GCF_014836415.1_ASM1483641v1_genomic.fna.gz | prodigal -d GCF_014836415.1_ASM1483641v1_genomic.fna/cds.fna -a GCF_014836415.1_ASM1483641v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:28:14,122] [INFO] Task succeeded: Prodigal
[2024-01-25 20:28:14,122] [INFO] Task started: HMMsearch
[2024-01-25 20:28:14,122] [INFO] Running command: hmmsearch --tblout GCF_014836415.1_ASM1483641v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9c5a909-e11f-425d-a3b8-e14182510ecd/dqc_reference/reference_markers.hmm GCF_014836415.1_ASM1483641v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:28:14,367] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:28:14,369] [INFO] Found 6/6 markers.
[2024-01-25 20:28:14,396] [INFO] Query marker FASTA was written to GCF_014836415.1_ASM1483641v1_genomic.fna/markers.fasta
[2024-01-25 20:28:14,397] [INFO] Task started: Blastn
[2024-01-25 20:28:14,397] [INFO] Running command: blastn -query GCF_014836415.1_ASM1483641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c5a909-e11f-425d-a3b8-e14182510ecd/dqc_reference/reference_markers.fasta -out GCF_014836415.1_ASM1483641v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:14,950] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:14,953] [INFO] Selected 18 target genomes.
[2024-01-25 20:28:14,953] [INFO] Target genome list was writen to GCF_014836415.1_ASM1483641v1_genomic.fna/target_genomes.txt
[2024-01-25 20:28:14,969] [INFO] Task started: fastANI
[2024-01-25 20:28:14,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg6500c039-2568-4937-8688-9d46e5580930/GCF_014836415.1_ASM1483641v1_genomic.fna.gz --refList GCF_014836415.1_ASM1483641v1_genomic.fna/target_genomes.txt --output GCF_014836415.1_ASM1483641v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:28:27,040] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:27,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9c5a909-e11f-425d-a3b8-e14182510ecd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:28:27,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9c5a909-e11f-425d-a3b8-e14182510ecd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:28:27,048] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:28:27,049] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:28:27,049] [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 gallistercoris	strain=Sa3CUA8	GCA_014836415.1	2762245	2762245	type	True	100.0	1034	1034	95	conclusive
Sporosarcina ureae	strain=DSM 2281	GCA_000425545.1	1571	1571	suspected-type	True	77.524	81	1034	95	below_threshold
Sporosarcina limicola	strain=DSM 13886	GCA_014873855.1	34101	34101	type	True	77.3852	91	1034	95	below_threshold
Sporosarcina luteola	strain=NBRC 105378	GCA_007991495.1	582850	582850	type	True	77.2959	106	1034	95	below_threshold
Filibacter tadaridae		GCA_900609045.1	2483811	2483811	type	True	77.2372	98	1034	95	below_threshold
Paenisporosarcina indica	strain=PN2	GCA_001939075.1	650093	650093	type	True	76.8619	53	1034	95	below_threshold
Sporosarcina jiandibaonis	strain=LAM9210	GCA_013184495.1	2715535	2715535	type	True	76.7871	58	1034	95	below_threshold
Planococcus glaciei	strain=CGMCC 1.6846	GCA_900099655.1	459472	459472	type	True	76.7855	51	1034	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:28:27,051] [INFO] DFAST Taxonomy check result was written to GCF_014836415.1_ASM1483641v1_genomic.fna/tc_result.tsv
[2024-01-25 20:28:27,051] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:28:27,051] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:28:27,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9c5a909-e11f-425d-a3b8-e14182510ecd/dqc_reference/checkm_data
[2024-01-25 20:28:27,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:28:27,090] [INFO] Task started: CheckM
[2024-01-25 20:28:27,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836415.1_ASM1483641v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836415.1_ASM1483641v1_genomic.fna/checkm_input GCF_014836415.1_ASM1483641v1_genomic.fna/checkm_result
[2024-01-25 20:28:53,567] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:53,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:53,589] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:53,589] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:53,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836415.1_ASM1483641v1_genomic.fna/markers.fasta)
[2024-01-25 20:28:53,590] [INFO] Task started: Blastn
[2024-01-25 20:28:53,590] [INFO] Running command: blastn -query GCF_014836415.1_ASM1483641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c5a909-e11f-425d-a3b8-e14182510ecd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836415.1_ASM1483641v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:54,401] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:54,405] [INFO] Selected 12 target genomes.
[2024-01-25 20:28:54,405] [INFO] Target genome list was writen to GCF_014836415.1_ASM1483641v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:54,415] [INFO] Task started: fastANI
[2024-01-25 20:28:54,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg6500c039-2568-4937-8688-9d46e5580930/GCF_014836415.1_ASM1483641v1_genomic.fna.gz --refList GCF_014836415.1_ASM1483641v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836415.1_ASM1483641v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:29:03,138] [INFO] Task succeeded: fastANI
[2024-01-25 20:29:03,145] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:29:03,145] [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_014836415.1	s__Sporosarcina sp014836415	100.0	1034	1034	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000813425.1	s__Sporosarcina sp000813425	84.9122	829	1034	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	95.98	95.98	0.89	0.89	2	-
GCF_003384035.1	s__Sporosarcina sp003384035	84.6382	808	1034	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_000586555.1	s__Sporosarcina sp000586555	84.5478	836	1034	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_016820585.1	s__Sporosarcina sp016820585	77.5774	90	1034	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_000829195.1	s__Sporosarcina sp000829195	77.5339	80	1034	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_008369195.1	s__Sporosarcina sp008369195	77.3953	92	1034	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	77.3921	90	1034	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_007991495.1	s__Sporosarcina luteola	77.2918	106	1034	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_900609045.1	s__Sporosarcina tadaridae	77.2084	99	1034	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:29:03,146] [INFO] GTDB search result was written to GCF_014836415.1_ASM1483641v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:29:03,147] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:29:03,149] [INFO] DFAST_QC result json was written to GCF_014836415.1_ASM1483641v1_genomic.fna/dqc_result.json
[2024-01-25 20:29:03,149] [INFO] DFAST_QC completed!
[2024-01-25 20:29:03,149] [INFO] Total running time: 0h0m57s