[2023-03-18 23:03:14,061] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:03:14,062] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:03:14,063] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ec5ba19-0539-4bb9-a559-1906f46713bf/dqc_reference
[2023-03-18 23:03:15,188] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:03:15,189] [INFO] Task started: Prodigal
[2023-03-18 23:03:15,189] [INFO] Running command: cat /var/lib/cwl/stg1bd16fc0-27fa-4fa3-a9c9-c87169e0db56/OceanDNA-b11346.fa | prodigal -d OceanDNA-b11346/cds.fna -a OceanDNA-b11346/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:03:29,520] [INFO] Task succeeded: Prodigal
[2023-03-18 23:03:29,520] [INFO] Task started: HMMsearch
[2023-03-18 23:03:29,520] [INFO] Running command: hmmsearch --tblout OceanDNA-b11346/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ec5ba19-0539-4bb9-a559-1906f46713bf/dqc_reference/reference_markers.hmm OceanDNA-b11346/protein.faa > /dev/null
[2023-03-18 23:03:29,700] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:03:29,701] [INFO] Found 6/6 markers.
[2023-03-18 23:03:29,721] [INFO] Query marker FASTA was written to OceanDNA-b11346/markers.fasta
[2023-03-18 23:03:29,722] [INFO] Task started: Blastn
[2023-03-18 23:03:29,722] [INFO] Running command: blastn -query OceanDNA-b11346/markers.fasta -db /var/lib/cwl/stg2ec5ba19-0539-4bb9-a559-1906f46713bf/dqc_reference/reference_markers.fasta -out OceanDNA-b11346/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:03:30,289] [INFO] Task succeeded: Blastn
[2023-03-18 23:03:30,293] [INFO] Selected 22 target genomes.
[2023-03-18 23:03:30,293] [INFO] Target genome list was writen to OceanDNA-b11346/target_genomes.txt
[2023-03-18 23:03:30,302] [INFO] Task started: fastANI
[2023-03-18 23:03:30,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bd16fc0-27fa-4fa3-a9c9-c87169e0db56/OceanDNA-b11346.fa --refList OceanDNA-b11346/target_genomes.txt --output OceanDNA-b11346/fastani_result.tsv --threads 1
[2023-03-18 23:03:45,095] [INFO] Task succeeded: fastANI
[2023-03-18 23:03:45,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ec5ba19-0539-4bb9-a559-1906f46713bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:03:45,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ec5ba19-0539-4bb9-a559-1906f46713bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:03:45,104] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:03:45,104] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:03:45,104] [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
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	77.4599	172	690	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.4206	176	690	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	77.3821	146	690	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	76.9945	85	690	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.8156	101	690	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	76.7551	60	690	95	below_threshold
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	76.7412	87	690	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	76.734	66	690	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	76.4277	84	690	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.3867	62	690	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	76.2701	74	690	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.0304	93	690	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	75.8402	66	690	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:03:45,106] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11346/tc_result.tsv
[2023-03-18 23:03:45,107] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:03:45,107] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:03:45,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ec5ba19-0539-4bb9-a559-1906f46713bf/dqc_reference/checkm_data
[2023-03-18 23:03:45,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:03:45,113] [INFO] Task started: CheckM
[2023-03-18 23:03:45,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11346/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11346/checkm_input OceanDNA-b11346/checkm_result
[2023-03-18 23:04:24,248] [INFO] Task succeeded: CheckM
[2023-03-18 23:04:24,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:04:24,251] [INFO] ===== Completeness check finished =====
[2023-03-18 23:04:24,251] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:04:24,251] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11346/markers.fasta)
[2023-03-18 23:04:24,252] [INFO] Task started: Blastn
[2023-03-18 23:04:24,252] [INFO] Running command: blastn -query OceanDNA-b11346/markers.fasta -db /var/lib/cwl/stg2ec5ba19-0539-4bb9-a559-1906f46713bf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11346/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:04:25,039] [INFO] Task succeeded: Blastn
[2023-03-18 23:04:25,040] [INFO] Selected 24 target genomes.
[2023-03-18 23:04:25,040] [INFO] Target genome list was writen to OceanDNA-b11346/target_genomes_gtdb.txt
[2023-03-18 23:04:25,064] [INFO] Task started: fastANI
[2023-03-18 23:04:25,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bd16fc0-27fa-4fa3-a9c9-c87169e0db56/OceanDNA-b11346.fa --refList OceanDNA-b11346/target_genomes_gtdb.txt --output OceanDNA-b11346/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:04:37,669] [INFO] Task succeeded: fastANI
[2023-03-18 23:04:37,679] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:04:37,679] [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_900102055.1	s__Ulvibacter litoralis	77.4599	172	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003688405.1	s__Ulvibacter antarcticus	77.3821	146	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974325.1	s__Patiriisocius marinus	76.9945	85	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	76.8156	101	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	76.7551	60	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCA_018669795.1	s__GCA-002733185 sp018669795	76.7536	103	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	98.54	95.82	0.94	0.91	4	-
GCF_009014635.1	s__Patiriisocius marinistellae	76.7412	87	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900489465.1	s__Aequorivita sp900489465	76.6792	83	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649715.1	s__Aequorivita sp016649715	76.6088	56	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	76.5788	95	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265385.1	s__Aequorivita sublithincola	76.4277	84	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715485.1	s__Aequorivita sp002715485	76.38	79	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_000429125.1	s__Aequorivita capsosiphonis	76.2701	74	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694465.1	s__IN17 sp002694465	76.1969	82	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
GCF_003143755.1	s__Algibacter_B sp003143755	76.1677	53	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375495.1	s__Marinirhabdus sp002375495	76.1617	63	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCF_008084905.1	s__Xanthomarina maritima	75.8236	72	690	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:04:37,679] [INFO] GTDB search result was written to OceanDNA-b11346/result_gtdb.tsv
[2023-03-18 23:04:37,679] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:04:37,681] [INFO] DFAST_QC result json was written to OceanDNA-b11346/dqc_result.json
[2023-03-18 23:04:37,681] [INFO] DFAST_QC completed!
[2023-03-18 23:04:37,681] [INFO] Total running time: 0h1m24s