[2024-01-24 13:31:57,173] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,175] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,176] [INFO] DQC Reference Directory: /var/lib/cwl/stgd09cd803-d870-465a-9cb4-ad786e570d76/dqc_reference
[2024-01-24 13:31:58,529] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:58,530] [INFO] Task started: Prodigal
[2024-01-24 13:31:58,530] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9f1448a-12e9-4fd1-b31e-62db6c18baa3/GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/cds.fna -a GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:05,669] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:05,669] [INFO] Task started: HMMsearch
[2024-01-24 13:32:05,670] [INFO] Running command: hmmsearch --tblout GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd09cd803-d870-465a-9cb4-ad786e570d76/dqc_reference/reference_markers.hmm GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:05,951] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:05,953] [INFO] Found 6/6 markers.
[2024-01-24 13:32:05,995] [INFO] Query marker FASTA was written to GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:32:05,996] [INFO] Task started: Blastn
[2024-01-24 13:32:05,996] [INFO] Running command: blastn -query GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd09cd803-d870-465a-9cb4-ad786e570d76/dqc_reference/reference_markers.fasta -out GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:06,620] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:06,623] [INFO] Selected 24 target genomes.
[2024-01-24 13:32:06,624] [INFO] Target genome list was writen to GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:32:06,634] [INFO] Task started: fastANI
[2024-01-24 13:32:06,635] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9f1448a-12e9-4fd1-b31e-62db6c18baa3/GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna.gz --refList GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:20,301] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:20,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd09cd803-d870-465a-9cb4-ad786e570d76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:20,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd09cd803-d870-465a-9cb4-ad786e570d76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:20,312] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:20,313] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:20,313] [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
Salinibacillus kushneri	strain=CGMCC 1.3566	GCA_900111405.1	237682	237682	type	True	100.0	1146	1149	95	conclusive
Salinibacillus xinjiangensis	strain=J4	GCA_009649735.1	1229268	1229268	type	True	77.7013	253	1149	95	below_threshold
Tenuibacillus multivorans	strain=CGMCC 1.3442	GCA_900103915.1	237069	237069	type	True	76.6518	53	1149	95	below_threshold
Piscibacillus halophilus	strain=DSM 21633	GCA_900110685.1	571933	571933	type	True	76.618	55	1149	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	76.6113	55	1149	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	76.4187	57	1149	95	below_threshold
Melghiribacillus thermohalophilus	strain=DSM 25894	GCA_004342905.1	1324956	1324956	type	True	76.3454	61	1149	95	below_threshold
Oceanobacillus neutriphilus	strain=CGMCC 1.7693	GCA_014645515.1	531815	531815	type	True	76.1721	59	1149	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_009659515.1	563735	563735	type	True	76.1659	66	1149	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	76.1433	54	1149	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_010994055.1	563735	563735	type	True	75.9722	64	1149	95	below_threshold
Bacillus andreraoultii	strain=SIT1	GCA_001244735.1	1499685	1499685	type	True	75.874	54	1149	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	75.7808	66	1149	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:20,314] [INFO] DFAST Taxonomy check result was written to GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:32:20,315] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:20,315] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:20,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd09cd803-d870-465a-9cb4-ad786e570d76/dqc_reference/checkm_data
[2024-01-24 13:32:20,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:20,351] [INFO] Task started: CheckM
[2024-01-24 13:32:20,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/checkm_input GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:32:48,002] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:48,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:48,024] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:48,025] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:48,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:32:48,026] [INFO] Task started: Blastn
[2024-01-24 13:32:48,026] [INFO] Running command: blastn -query GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd09cd803-d870-465a-9cb4-ad786e570d76/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:48,798] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:48,802] [INFO] Selected 24 target genomes.
[2024-01-24 13:32:48,803] [INFO] Target genome list was writen to GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:48,821] [INFO] Task started: fastANI
[2024-01-24 13:32:48,822] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9f1448a-12e9-4fd1-b31e-62db6c18baa3/GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna.gz --refList GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:04,188] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:04,204] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:04,204] [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_900111405.1	s__Salinibacillus kushneri	100.0	1146	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salinibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010092505.1	s__Salinibacillus sp010092505	79.5502	561	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649735.1	s__Salinibacillus xinjiangensis	77.7116	253	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017656265.1	s__Melghiribacillus sp017656265	76.7257	68	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Melghiribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083865.1	s__Paraliobacillus salinarum	76.6113	55	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377765.1	s__Gracilibacillus lacisalsi	76.5845	57	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	-
GCF_900103915.1	s__Tenuibacillus multivorans	76.5812	52	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Tenuibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900240405.1	s__OEQK01 sp900240405	76.562	127	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__OEQK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342905.1	s__Melghiribacillus thermohalophilus	76.3454	61	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Melghiribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515705.1	s__Oceanobacillus profundus	76.3131	63	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.49	99.20	0.93	0.85	4	-
GCF_014645515.1	s__Oceanobacillus neutriphilus	76.1721	59	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014637405.1	s__Ornithinibacillus halotolerans	76.1433	54	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001244735.1	s__Bacillus_J andreraoultii	75.7407	51	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_J	95.0	100.00	100.00	0.99	0.99	4	-
GCF_014638995.1	s__Virgibacillus_E oceani	75.7319	65	1149	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:04,206] [INFO] GTDB search result was written to GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:04,206] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:04,210] [INFO] DFAST_QC result json was written to GCF_900111405.1_IMG-taxon_2675903136_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:33:04,210] [INFO] DFAST_QC completed!
[2024-01-24 13:33:04,210] [INFO] Total running time: 0h1m7s