[2024-01-24 12:13:28,651] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,663] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,663] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4a77294-ae9c-4ffb-8e92-4e9e80af121d/dqc_reference
[2024-01-24 12:13:30,128] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,129] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,129] [INFO] Running command: gunzip -c /var/lib/cwl/stga23c7793-ab0f-4c0c-8421-7837ced70e92/GCF_001050375.1_ASM105037v1_genomic.fna.gz | prodigal -d GCF_001050375.1_ASM105037v1_genomic.fna/cds.fna -a GCF_001050375.1_ASM105037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:38,759] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:38,760] [INFO] Task started: HMMsearch
[2024-01-24 12:13:38,760] [INFO] Running command: hmmsearch --tblout GCF_001050375.1_ASM105037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4a77294-ae9c-4ffb-8e92-4e9e80af121d/dqc_reference/reference_markers.hmm GCF_001050375.1_ASM105037v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:39,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:39,144] [INFO] Found 6/6 markers.
[2024-01-24 12:13:39,189] [INFO] Query marker FASTA was written to GCF_001050375.1_ASM105037v1_genomic.fna/markers.fasta
[2024-01-24 12:13:39,189] [INFO] Task started: Blastn
[2024-01-24 12:13:39,189] [INFO] Running command: blastn -query GCF_001050375.1_ASM105037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4a77294-ae9c-4ffb-8e92-4e9e80af121d/dqc_reference/reference_markers.fasta -out GCF_001050375.1_ASM105037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:39,964] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:39,967] [INFO] Selected 23 target genomes.
[2024-01-24 12:13:39,967] [INFO] Target genome list was writen to GCF_001050375.1_ASM105037v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:39,974] [INFO] Task started: fastANI
[2024-01-24 12:13:39,974] [INFO] Running command: fastANI --query /var/lib/cwl/stga23c7793-ab0f-4c0c-8421-7837ced70e92/GCF_001050375.1_ASM105037v1_genomic.fna.gz --refList GCF_001050375.1_ASM105037v1_genomic.fna/target_genomes.txt --output GCF_001050375.1_ASM105037v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:57,415] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:57,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4a77294-ae9c-4ffb-8e92-4e9e80af121d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:57,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4a77294-ae9c-4ffb-8e92-4e9e80af121d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:57,435] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:57,435] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:57,435] [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
Catenovulum maritimum	strain=Q1	GCA_001050375.1	1513271	1513271	type	True	100.0	1491	1491	95	conclusive
Catenovulum agarivorans	strain=YM01	GCA_000281085.1	1172192	1172192	type	True	78.7805	265	1491	95	below_threshold
Saccharobesus litoralis	strain=CCB-QB4	GCA_003063625.1	2172099	2172099	type	True	77.7768	155	1491	95	below_threshold
Gayadomonas joobiniege	strain=G7	GCA_000300815.1	1234606	1234606	type	True	77.5572	121	1491	95	below_threshold
Marinifaba aquimaris	strain=SM1970	GCA_013328345.1	2741323	2741323	type	True	77.4847	127	1491	95	below_threshold
Pseudoalteromonas ulvae	strain=UL12	GCA_014925405.1	107327	107327	type	True	77.3653	78	1491	95	below_threshold
Moritella marina	strain=MP-1	GCA_000381865.1	90736	90736	type	True	76.6841	56	1491	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	76.6336	83	1491	95	below_threshold
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	76.5693	69	1491	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	76.5403	70	1491	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	76.4363	91	1491	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	76.3234	69	1491	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	76.1195	65	1491	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	75.9178	62	1491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:57,443] [INFO] DFAST Taxonomy check result was written to GCF_001050375.1_ASM105037v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:57,448] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:57,448] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:57,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4a77294-ae9c-4ffb-8e92-4e9e80af121d/dqc_reference/checkm_data
[2024-01-24 12:13:57,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:57,503] [INFO] Task started: CheckM
[2024-01-24 12:13:57,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001050375.1_ASM105037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001050375.1_ASM105037v1_genomic.fna/checkm_input GCF_001050375.1_ASM105037v1_genomic.fna/checkm_result
[2024-01-24 12:14:29,754] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:29,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:29,784] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:29,784] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:29,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001050375.1_ASM105037v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:29,785] [INFO] Task started: Blastn
[2024-01-24 12:14:29,785] [INFO] Running command: blastn -query GCF_001050375.1_ASM105037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4a77294-ae9c-4ffb-8e92-4e9e80af121d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001050375.1_ASM105037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:31,001] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:31,005] [INFO] Selected 19 target genomes.
[2024-01-24 12:14:31,005] [INFO] Target genome list was writen to GCF_001050375.1_ASM105037v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:31,021] [INFO] Task started: fastANI
[2024-01-24 12:14:31,022] [INFO] Running command: fastANI --query /var/lib/cwl/stga23c7793-ab0f-4c0c-8421-7837ced70e92/GCF_001050375.1_ASM105037v1_genomic.fna.gz --refList GCF_001050375.1_ASM105037v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001050375.1_ASM105037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:45,062] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:45,082] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:45,082] [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_001050375.1	s__Catenovulum maritimum	100.0	1491	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000281085.1	s__Catenovulum agarivorans	78.7959	264	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000568405.1	s__Catenovulum agarivorans_A	78.5857	237	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063625.1	s__Algibacillus sp003063625	77.8239	154	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Algibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007289895.1	s__Catenovulum sediminis	77.7284	171	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300815.1	s__Catenovulum joobiniege	77.5572	121	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328345.1	s__Marinifaba aquimaris	77.4628	128	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Marinifaba	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925405.1	s__Pseudoalteromonas ulvae	77.3653	78	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.81	98.81	0.93	0.93	2	-
GCF_002843355.2	s__Colwellia echini	76.6336	83	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001444405.1	s__Pseudoalteromonas phenolica	76.5411	70	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.52	98.61	0.97	0.92	4	-
GCA_015491935.1	s__GCA-2401725 sp015491935	76.5126	61	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498095.1	s__Pseudoalteromonas sp000498095	76.4587	62	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.86	97.76	0.88	0.87	3	-
GCF_002000085.1	s__Pseudocolwellia agarivorans	76.4363	91	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudocolwellia	95.0	95.36	95.36	0.90	0.90	2	-
GCF_014641855.1	s__Shewanella inventionis	76.0152	52	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:45,086] [INFO] GTDB search result was written to GCF_001050375.1_ASM105037v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:45,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:45,091] [INFO] DFAST_QC result json was written to GCF_001050375.1_ASM105037v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:45,092] [INFO] DFAST_QC completed!
[2024-01-24 12:14:45,092] [INFO] Total running time: 0h1m16s