[2024-01-25 17:58:35,651] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:35,655] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:35,655] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a6c2acc-acc9-42e7-ba48-bb738a4523ec/dqc_reference
[2024-01-25 17:58:36,851] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:36,851] [INFO] Task started: Prodigal
[2024-01-25 17:58:36,852] [INFO] Running command: gunzip -c /var/lib/cwl/stgea6d4dd3-1feb-487a-a6fa-96e03c30be4d/GCF_900457495.1_53694_E01_genomic.fna.gz | prodigal -d GCF_900457495.1_53694_E01_genomic.fna/cds.fna -a GCF_900457495.1_53694_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:58:43,524] [INFO] Task succeeded: Prodigal
[2024-01-25 17:58:43,525] [INFO] Task started: HMMsearch
[2024-01-25 17:58:43,525] [INFO] Running command: hmmsearch --tblout GCF_900457495.1_53694_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a6c2acc-acc9-42e7-ba48-bb738a4523ec/dqc_reference/reference_markers.hmm GCF_900457495.1_53694_E01_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:58:43,755] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:58:43,756] [INFO] Found 6/6 markers.
[2024-01-25 17:58:43,785] [INFO] Query marker FASTA was written to GCF_900457495.1_53694_E01_genomic.fna/markers.fasta
[2024-01-25 17:58:43,786] [INFO] Task started: Blastn
[2024-01-25 17:58:43,786] [INFO] Running command: blastn -query GCF_900457495.1_53694_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a6c2acc-acc9-42e7-ba48-bb738a4523ec/dqc_reference/reference_markers.fasta -out GCF_900457495.1_53694_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:58:44,332] [INFO] Task succeeded: Blastn
[2024-01-25 17:58:44,335] [INFO] Selected 30 target genomes.
[2024-01-25 17:58:44,335] [INFO] Target genome list was writen to GCF_900457495.1_53694_E01_genomic.fna/target_genomes.txt
[2024-01-25 17:58:44,347] [INFO] Task started: fastANI
[2024-01-25 17:58:44,347] [INFO] Running command: fastANI --query /var/lib/cwl/stgea6d4dd3-1feb-487a-a6fa-96e03c30be4d/GCF_900457495.1_53694_E01_genomic.fna.gz --refList GCF_900457495.1_53694_E01_genomic.fna/target_genomes.txt --output GCF_900457495.1_53694_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:02,369] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:02,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a6c2acc-acc9-42e7-ba48-bb738a4523ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:02,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a6c2acc-acc9-42e7-ba48-bb738a4523ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:02,378] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:59:02,379] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:59:02,379] [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	100.0	1102	1102	95	conclusive
Sporosarcina ureilytica	strain=LMG 22257	GCA_001753205.1	298596	298596	type	True	90.0966	881	1102	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	79.6892	56	1102	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	78.8054	90	1102	95	below_threshold
Sporosarcina jiandibaonis	strain=LAM9210	GCA_013184495.1	2715535	2715535	type	True	77.8433	252	1102	95	below_threshold
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	77.6983	80	1102	95	below_threshold
Sporosarcina limicola	strain=DSM 13886	GCA_014873855.1	34101	34101	type	True	77.2882	104	1102	95	below_threshold
Filibacter tadaridae		GCA_900609045.1	2483811	2483811	type	True	77.0832	114	1102	95	below_threshold
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	76.8258	84	1102	95	below_threshold
Psychrobacillus lasiicapitis	strain=CGMCC 1.15308	GCA_014641675.1	1636719	1636719	type	True	76.7736	88	1102	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	76.1202	59	1102	95	below_threshold
Ureibacillus thermosphaericus	strain=DSM 10633	GCA_012396605.1	51173	51173	type	True	75.6949	52	1102	95	below_threshold
Ureibacillus thermosphaericus	strain=DSM 10633	GCA_014202525.1	51173	51173	type	True	75.6905	53	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:02,380] [INFO] DFAST Taxonomy check result was written to GCF_900457495.1_53694_E01_genomic.fna/tc_result.tsv
[2024-01-25 17:59:02,381] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:02,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:02,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a6c2acc-acc9-42e7-ba48-bb738a4523ec/dqc_reference/checkm_data
[2024-01-25 17:59:02,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:02,414] [INFO] Task started: CheckM
[2024-01-25 17:59:02,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900457495.1_53694_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900457495.1_53694_E01_genomic.fna/checkm_input GCF_900457495.1_53694_E01_genomic.fna/checkm_result
[2024-01-25 17:59:26,841] [INFO] Task succeeded: CheckM
[2024-01-25 17:59:26,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:59:26,878] [INFO] ===== Completeness check finished =====
[2024-01-25 17:59:26,878] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:59:26,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900457495.1_53694_E01_genomic.fna/markers.fasta)
[2024-01-25 17:59:26,879] [INFO] Task started: Blastn
[2024-01-25 17:59:26,879] [INFO] Running command: blastn -query GCF_900457495.1_53694_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a6c2acc-acc9-42e7-ba48-bb738a4523ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_900457495.1_53694_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:27,706] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:27,713] [INFO] Selected 22 target genomes.
[2024-01-25 17:59:27,713] [INFO] Target genome list was writen to GCF_900457495.1_53694_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:59:27,738] [INFO] Task started: fastANI
[2024-01-25 17:59:27,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgea6d4dd3-1feb-487a-a6fa-96e03c30be4d/GCF_900457495.1_53694_E01_genomic.fna.gz --refList GCF_900457495.1_53694_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900457495.1_53694_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:59:43,015] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:43,025] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:59:43,025] [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	100.0	1102	1102	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	90.1075	882	1102	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_009720625.1	s__Metabacillus sp004801455	79.8442	58	1102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018140925.1	s__Psychrobacillus sp018140925	79.5853	79	1102	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_013184495.1	s__Sporosarcina sp013184495	77.8604	250	1102	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	77.7016	222	1102	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	77.6881	81	1102	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_001563475.1	s__Sporosarcina sp001563475	77.4395	153	1102	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	77.2882	104	1102	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	77.2387	128	1102	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_014282005.1	s__Sporosarcina sp014282005	77.1973	131	1102	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_900609045.1	s__Sporosarcina tadaridae	77.1341	116	1102	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	76.9688	84	1102	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	76.4801	95	1102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:59:43,026] [INFO] GTDB search result was written to GCF_900457495.1_53694_E01_genomic.fna/result_gtdb.tsv
[2024-01-25 17:59:43,027] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:59:43,030] [INFO] DFAST_QC result json was written to GCF_900457495.1_53694_E01_genomic.fna/dqc_result.json
[2024-01-25 17:59:43,030] [INFO] DFAST_QC completed!
[2024-01-25 17:59:43,030] [INFO] Total running time: 0h1m7s