[2024-01-24 11:51:11,115] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,118] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg597ce983-4fa2-4e15-a884-806b0cca90ba/dqc_reference
[2024-01-24 11:51:12,495] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,496] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,496] [INFO] Running command: gunzip -c /var/lib/cwl/stg482d0316-f623-4574-a847-cdbcfda84407/GCF_900609045.1_aTB-66_genomic.fna.gz | prodigal -d GCF_900609045.1_aTB-66_genomic.fna/cds.fna -a GCF_900609045.1_aTB-66_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:19,934] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:19,935] [INFO] Task started: HMMsearch
[2024-01-24 11:51:19,935] [INFO] Running command: hmmsearch --tblout GCF_900609045.1_aTB-66_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg597ce983-4fa2-4e15-a884-806b0cca90ba/dqc_reference/reference_markers.hmm GCF_900609045.1_aTB-66_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:20,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:20,250] [INFO] Found 6/6 markers.
[2024-01-24 11:51:20,288] [INFO] Query marker FASTA was written to GCF_900609045.1_aTB-66_genomic.fna/markers.fasta
[2024-01-24 11:51:20,288] [INFO] Task started: Blastn
[2024-01-24 11:51:20,289] [INFO] Running command: blastn -query GCF_900609045.1_aTB-66_genomic.fna/markers.fasta -db /var/lib/cwl/stg597ce983-4fa2-4e15-a884-806b0cca90ba/dqc_reference/reference_markers.fasta -out GCF_900609045.1_aTB-66_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:20,926] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:20,930] [INFO] Selected 22 target genomes.
[2024-01-24 11:51:20,930] [INFO] Target genome list was writen to GCF_900609045.1_aTB-66_genomic.fna/target_genomes.txt
[2024-01-24 11:51:20,938] [INFO] Task started: fastANI
[2024-01-24 11:51:20,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg482d0316-f623-4574-a847-cdbcfda84407/GCF_900609045.1_aTB-66_genomic.fna.gz --refList GCF_900609045.1_aTB-66_genomic.fna/target_genomes.txt --output GCF_900609045.1_aTB-66_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:34,354] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:34,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg597ce983-4fa2-4e15-a884-806b0cca90ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:34,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg597ce983-4fa2-4e15-a884-806b0cca90ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:34,364] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:34,364] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:34,365] [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
Filibacter tadaridae		GCA_900609045.1	2483811	2483811	type	True	100.0	1011	1012	95	conclusive
Sporosarcina limicola	strain=DSM 13886	GCA_014873855.1	34101	34101	type	True	78.2523	299	1012	95	below_threshold
Sporosarcina luteola	strain=NBRC 105378	GCA_007991495.1	582850	582850	type	True	77.4505	164	1012	95	below_threshold
Sporosarcina quadrami	strain=Sa2YVA2	GCA_014836615.1	2762234	2762234	type	True	77.4436	161	1012	95	below_threshold
Sporosarcina ureae	strain=DSM 2281	GCA_000425545.1	1571	1571	suspected-type	True	77.1618	92	1012	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	77.1575	78	1012	95	below_threshold
Sporosarcina jiandibaonis	strain=LAM9210	GCA_013184495.1	2715535	2715535	type	True	77.0208	129	1012	95	below_threshold
Sporosarcina gallistercoris	strain=Sa3CUA8	GCA_014836415.1	2762245	2762245	type	True	77.012	102	1012	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	76.4841	62	1012	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:34,367] [INFO] DFAST Taxonomy check result was written to GCF_900609045.1_aTB-66_genomic.fna/tc_result.tsv
[2024-01-24 11:51:34,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:34,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:34,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg597ce983-4fa2-4e15-a884-806b0cca90ba/dqc_reference/checkm_data
[2024-01-24 11:51:34,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:34,401] [INFO] Task started: CheckM
[2024-01-24 11:51:34,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900609045.1_aTB-66_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900609045.1_aTB-66_genomic.fna/checkm_input GCF_900609045.1_aTB-66_genomic.fna/checkm_result
[2024-01-24 11:52:01,863] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:01,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:01,881] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:01,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:01,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900609045.1_aTB-66_genomic.fna/markers.fasta)
[2024-01-24 11:52:01,882] [INFO] Task started: Blastn
[2024-01-24 11:52:01,882] [INFO] Running command: blastn -query GCF_900609045.1_aTB-66_genomic.fna/markers.fasta -db /var/lib/cwl/stg597ce983-4fa2-4e15-a884-806b0cca90ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_900609045.1_aTB-66_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:02,674] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:02,677] [INFO] Selected 19 target genomes.
[2024-01-24 11:52:02,678] [INFO] Target genome list was writen to GCF_900609045.1_aTB-66_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:02,691] [INFO] Task started: fastANI
[2024-01-24 11:52:02,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg482d0316-f623-4574-a847-cdbcfda84407/GCF_900609045.1_aTB-66_genomic.fna.gz --refList GCF_900609045.1_aTB-66_genomic.fna/target_genomes_gtdb.txt --output GCF_900609045.1_aTB-66_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:15,864] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:15,875] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:15,876] [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_900609045.1	s__Sporosarcina tadaridae	100.0	1011	1012	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_017347095.1	s__Sporosarcina sp017347095	78.4253	330	1012	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	78.2907	330	1012	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	78.2652	298	1012	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_001590685.1	s__Sporosarcina psychrophila	78.2024	351	1012	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_016820585.1	s__Sporosarcina sp016820585	78.2012	260	1012	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	78.1378	328	1012	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_013408665.1	s__Sporosarcina sp013408665	78.1117	312	1012	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_014836615.1	s__Sporosarcina sp014836615	77.4611	160	1012	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	77.4359	165	1012	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_003384035.1	s__Sporosarcina sp003384035	77.3361	97	1012	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	77.0881	164	1012	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_014836415.1	s__Sporosarcina sp014836415	77.0383	101	1012	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_004367585.1	s__Paenisporosarcina antarctica	76.6439	64	1012	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	95.47	95.47	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:15,877] [INFO] GTDB search result was written to GCF_900609045.1_aTB-66_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:15,879] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:15,882] [INFO] DFAST_QC result json was written to GCF_900609045.1_aTB-66_genomic.fna/dqc_result.json
[2024-01-24 11:52:15,882] [INFO] DFAST_QC completed!
[2024-01-24 11:52:15,882] [INFO] Total running time: 0h1m5s