[2023-03-15 10:52:57,302] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,302] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg468162b2-9b6b-4e0c-ad0e-b6b80ba1cc45/dqc_reference
[2023-03-15 10:52:58,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,863] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,864] [INFO] Running command: cat /var/lib/cwl/stge022b25e-6dc9-4bee-b298-ac5c73dfaaf5/OceanDNA-b6954.fa | prodigal -d OceanDNA-b6954/cds.fna -a OceanDNA-b6954/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:10,220] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:10,220] [INFO] Task started: HMMsearch
[2023-03-15 10:53:10,220] [INFO] Running command: hmmsearch --tblout OceanDNA-b6954/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg468162b2-9b6b-4e0c-ad0e-b6b80ba1cc45/dqc_reference/reference_markers.hmm OceanDNA-b6954/protein.faa > /dev/null
[2023-03-15 10:53:10,401] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:10,402] [INFO] Found 6/6 markers.
[2023-03-15 10:53:10,414] [INFO] Query marker FASTA was written to OceanDNA-b6954/markers.fasta
[2023-03-15 10:53:10,414] [INFO] Task started: Blastn
[2023-03-15 10:53:10,414] [INFO] Running command: blastn -query OceanDNA-b6954/markers.fasta -db /var/lib/cwl/stg468162b2-9b6b-4e0c-ad0e-b6b80ba1cc45/dqc_reference/reference_markers.fasta -out OceanDNA-b6954/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:10,970] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:10,971] [INFO] Selected 32 target genomes.
[2023-03-15 10:53:10,971] [INFO] Target genome list was writen to OceanDNA-b6954/target_genomes.txt
[2023-03-15 10:53:10,994] [INFO] Task started: fastANI
[2023-03-15 10:53:10,994] [INFO] Running command: fastANI --query /var/lib/cwl/stge022b25e-6dc9-4bee-b298-ac5c73dfaaf5/OceanDNA-b6954.fa --refList OceanDNA-b6954/target_genomes.txt --output OceanDNA-b6954/fastani_result.tsv --threads 1
[2023-03-15 10:53:28,879] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:28,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg468162b2-9b6b-4e0c-ad0e-b6b80ba1cc45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:28,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg468162b2-9b6b-4e0c-ad0e-b6b80ba1cc45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:28,892] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:28,892] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:53:28,892] [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
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	76.5776	75	605	95	below_threshold
Aquimarina sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	76.5339	57	605	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.4582	64	605	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.4496	52	605	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.446	100	605	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.4409	98	605	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.4383	60	605	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.3048	53	605	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	76.2867	59	605	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.2671	51	605	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	76.1964	64	605	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.1625	53	605	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.1464	63	605	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	76.0898	54	605	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	76.0851	55	605	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	76.0591	70	605	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	76.0518	72	605	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	76.0378	67	605	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	76.0229	58	605	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	75.9537	62	605	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	75.9404	55	605	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	75.6955	69	605	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	75.4276	54	605	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:53:28,893] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6954/tc_result.tsv
[2023-03-15 10:53:28,893] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:28,893] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:28,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg468162b2-9b6b-4e0c-ad0e-b6b80ba1cc45/dqc_reference/checkm_data
[2023-03-15 10:53:28,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:29,001] [INFO] Task started: CheckM
[2023-03-15 10:53:29,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6954/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6954/checkm_input OceanDNA-b6954/checkm_result
[2023-03-15 10:54:01,382] [INFO] Task succeeded: CheckM
[2023-03-15 10:54:01,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.24%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 10:54:01,385] [INFO] ===== Completeness check finished =====
[2023-03-15 10:54:01,385] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:54:01,385] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6954/markers.fasta)
[2023-03-15 10:54:01,386] [INFO] Task started: Blastn
[2023-03-15 10:54:01,386] [INFO] Running command: blastn -query OceanDNA-b6954/markers.fasta -db /var/lib/cwl/stg468162b2-9b6b-4e0c-ad0e-b6b80ba1cc45/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6954/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:54:02,155] [INFO] Task succeeded: Blastn
[2023-03-15 10:54:02,155] [INFO] Selected 13 target genomes.
[2023-03-15 10:54:02,156] [INFO] Target genome list was writen to OceanDNA-b6954/target_genomes_gtdb.txt
[2023-03-15 10:54:02,171] [INFO] Task started: fastANI
[2023-03-15 10:54:02,171] [INFO] Running command: fastANI --query /var/lib/cwl/stge022b25e-6dc9-4bee-b298-ac5c73dfaaf5/OceanDNA-b6954.fa --refList OceanDNA-b6954/target_genomes_gtdb.txt --output OceanDNA-b6954/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:54:09,150] [INFO] Task succeeded: fastANI
[2023-03-15 10:54:09,157] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:54:09,157] [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
GCA_004213605.1	s__GCA-002733185 sp004213605	95.7744	386	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	95.79	95.79	0.89	0.89	2	conclusive
GCA_905181835.1	s__GCA-002733185 sp905181835	86.1425	541	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004214175.1	s__GCA-002733185 sp004214175	84.7339	336	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713705.1	s__GCA-002733185 sp002713705	78.7146	301	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	97.32	97.11	0.93	0.92	3	-
GCA_018669795.1	s__GCA-002733185 sp018669795	78.47	303	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	98.54	95.82	0.94	0.91	4	-
GCA_002733185.1	s__GCA-002733185 sp002733185	77.6892	184	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090365.1	s__GCA-002733185 sp019090365	76.6397	112	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635865.1	s__Winogradskyella haliclonae	76.2877	59	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741275.1	s__Winogradskyella endarachnes	76.2683	70	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	76.2418	53	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443675.1	s__Aquimarina sp003443675	76.178	54	605	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 10:54:09,157] [INFO] GTDB search result was written to OceanDNA-b6954/result_gtdb.tsv
[2023-03-15 10:54:09,157] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:54:09,159] [INFO] DFAST_QC result json was written to OceanDNA-b6954/dqc_result.json
[2023-03-15 10:54:09,159] [INFO] DFAST_QC completed!
[2023-03-15 10:54:09,160] [INFO] Total running time: 0h1m12s