[2024-01-24 13:21:10,820] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:10,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:10,823] [INFO] DQC Reference Directory: /var/lib/cwl/stga867cc50-de87-4fe3-8733-46d2c2b21859/dqc_reference
[2024-01-24 13:21:12,315] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,316] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,317] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3deda19-e59d-4ccb-a859-e851e164a5e4/GCF_014873855.1_ASM1487385v1_genomic.fna.gz | prodigal -d GCF_014873855.1_ASM1487385v1_genomic.fna/cds.fna -a GCF_014873855.1_ASM1487385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:22,135] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:22,135] [INFO] Task started: HMMsearch
[2024-01-24 13:21:22,136] [INFO] Running command: hmmsearch --tblout GCF_014873855.1_ASM1487385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga867cc50-de87-4fe3-8733-46d2c2b21859/dqc_reference/reference_markers.hmm GCF_014873855.1_ASM1487385v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:22,663] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:22,665] [INFO] Found 6/6 markers.
[2024-01-24 13:21:22,732] [INFO] Query marker FASTA was written to GCF_014873855.1_ASM1487385v1_genomic.fna/markers.fasta
[2024-01-24 13:21:22,733] [INFO] Task started: Blastn
[2024-01-24 13:21:22,733] [INFO] Running command: blastn -query GCF_014873855.1_ASM1487385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga867cc50-de87-4fe3-8733-46d2c2b21859/dqc_reference/reference_markers.fasta -out GCF_014873855.1_ASM1487385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:23,575] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:23,579] [INFO] Selected 23 target genomes.
[2024-01-24 13:21:23,580] [INFO] Target genome list was writen to GCF_014873855.1_ASM1487385v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:23,618] [INFO] Task started: fastANI
[2024-01-24 13:21:23,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3deda19-e59d-4ccb-a859-e851e164a5e4/GCF_014873855.1_ASM1487385v1_genomic.fna.gz --refList GCF_014873855.1_ASM1487385v1_genomic.fna/target_genomes.txt --output GCF_014873855.1_ASM1487385v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:37,883] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:37,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga867cc50-de87-4fe3-8733-46d2c2b21859/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:37,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga867cc50-de87-4fe3-8733-46d2c2b21859/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:37,897] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:21:37,897] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:21:37,898] [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 limicola	strain=DSM 13886	GCA_014873855.1	34101	34101	type	True	100.0	1387	1393	95	conclusive
Filibacter tadaridae		GCA_900609045.1	2483811	2483811	type	True	78.162	315	1393	95	below_threshold
Sporosarcina gallistercoris	strain=Sa3CUA8	GCA_014836415.1	2762245	2762245	type	True	77.6694	83	1393	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	77.6261	100	1393	95	below_threshold
Sporosarcina quadrami	strain=Sa2YVA2	GCA_014836615.1	2762234	2762234	type	True	77.556	159	1393	95	below_threshold
Sporosarcina luteola	strain=NBRC 105378	GCA_007991495.1	582850	582850	type	True	77.5312	163	1393	95	below_threshold
Sporosarcina pasteurii	strain=NCTC4822	GCA_900457495.1	1474	1474	type	True	77.1279	107	1393	95	below_threshold
Sporosarcina ureilytica	strain=LMG 22257	GCA_001753205.1	298596	298596	type	True	76.9463	123	1393	95	below_threshold
Sporosarcina jiandibaonis	strain=LAM9210	GCA_013184495.1	2715535	2715535	type	True	76.8238	159	1393	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	76.8085	63	1393	95	below_threshold
Paenisporosarcina indica	strain=PN2	GCA_001939075.1	650093	650093	type	True	76.7352	77	1393	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	76.2675	56	1393	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:37,903] [INFO] DFAST Taxonomy check result was written to GCF_014873855.1_ASM1487385v1_genomic.fna/tc_result.tsv
[2024-01-24 13:21:37,904] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:37,904] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:37,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga867cc50-de87-4fe3-8733-46d2c2b21859/dqc_reference/checkm_data
[2024-01-24 13:21:37,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:37,954] [INFO] Task started: CheckM
[2024-01-24 13:21:37,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014873855.1_ASM1487385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014873855.1_ASM1487385v1_genomic.fna/checkm_input GCF_014873855.1_ASM1487385v1_genomic.fna/checkm_result
[2024-01-24 13:22:16,891] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:16,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:16,923] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:16,924] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:16,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014873855.1_ASM1487385v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:16,925] [INFO] Task started: Blastn
[2024-01-24 13:22:16,925] [INFO] Running command: blastn -query GCF_014873855.1_ASM1487385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga867cc50-de87-4fe3-8733-46d2c2b21859/dqc_reference/reference_markers_gtdb.fasta -out GCF_014873855.1_ASM1487385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:17,760] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:17,768] [INFO] Selected 11 target genomes.
[2024-01-24 13:22:17,768] [INFO] Target genome list was writen to GCF_014873855.1_ASM1487385v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:17,780] [INFO] Task started: fastANI
[2024-01-24 13:22:17,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3deda19-e59d-4ccb-a859-e851e164a5e4/GCF_014873855.1_ASM1487385v1_genomic.fna.gz --refList GCF_014873855.1_ASM1487385v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014873855.1_ASM1487385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:26,569] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:26,582] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:26,583] [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_014873855.1	s__Sporosarcina limicola	100.0	1387	1393	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_001590685.1	s__Sporosarcina psychrophila	79.0715	462	1393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	98.26	98.26	0.89	0.89	2	-
GCF_014282005.1	s__Sporosarcina sp014282005	78.9499	403	1393	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_008369195.1	s__Sporosarcina sp008369195	78.9419	459	1393	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_017347095.1	s__Sporosarcina sp017347095	78.9051	443	1393	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_013408665.1	s__Sporosarcina sp013408665	78.6731	333	1393	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	78.6573	346	1393	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	78.1859	313	1393	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_002743255.1	s__Sporosarcina sp002743255	77.489	87	1393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	97.62	97.10	0.91	0.90	4	-
GCF_003351785.1	s__Sporosarcina sp003351785	77.1747	95	1393	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_001939075.1	s__Paenisporosarcina indica	76.7352	77	1393	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:26,586] [INFO] GTDB search result was written to GCF_014873855.1_ASM1487385v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:26,587] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:26,592] [INFO] DFAST_QC result json was written to GCF_014873855.1_ASM1487385v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:26,592] [INFO] DFAST_QC completed!
[2024-01-24 13:22:26,592] [INFO] Total running time: 0h1m16s