[2023-03-17 05:01:06,757] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:01:06,757] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:01:06,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cc6faa5-722f-4ac4-b734-2131ff86cb68/dqc_reference
[2023-03-17 05:01:08,511] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:01:08,511] [INFO] Task started: Prodigal
[2023-03-17 05:01:08,512] [INFO] Running command: cat /var/lib/cwl/stg2807d4d7-bf70-42fb-a670-dd9971049d57/OceanDNA-b11344.fa | prodigal -d OceanDNA-b11344/cds.fna -a OceanDNA-b11344/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:01:33,585] [INFO] Task succeeded: Prodigal
[2023-03-17 05:01:33,585] [INFO] Task started: HMMsearch
[2023-03-17 05:01:33,585] [INFO] Running command: hmmsearch --tblout OceanDNA-b11344/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cc6faa5-722f-4ac4-b734-2131ff86cb68/dqc_reference/reference_markers.hmm OceanDNA-b11344/protein.faa > /dev/null
[2023-03-17 05:01:33,796] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:01:33,796] [INFO] Found 6/6 markers.
[2023-03-17 05:01:33,820] [INFO] Query marker FASTA was written to OceanDNA-b11344/markers.fasta
[2023-03-17 05:01:33,820] [INFO] Task started: Blastn
[2023-03-17 05:01:33,820] [INFO] Running command: blastn -query OceanDNA-b11344/markers.fasta -db /var/lib/cwl/stg4cc6faa5-722f-4ac4-b734-2131ff86cb68/dqc_reference/reference_markers.fasta -out OceanDNA-b11344/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:01:34,386] [INFO] Task succeeded: Blastn
[2023-03-17 05:01:34,387] [INFO] Selected 19 target genomes.
[2023-03-17 05:01:34,387] [INFO] Target genome list was writen to OceanDNA-b11344/target_genomes.txt
[2023-03-17 05:01:34,400] [INFO] Task started: fastANI
[2023-03-17 05:01:34,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg2807d4d7-bf70-42fb-a670-dd9971049d57/OceanDNA-b11344.fa --refList OceanDNA-b11344/target_genomes.txt --output OceanDNA-b11344/fastani_result.tsv --threads 1
[2023-03-17 05:01:45,107] [INFO] Task succeeded: fastANI
[2023-03-17 05:01:45,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cc6faa5-722f-4ac4-b734-2131ff86cb68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:01:45,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cc6faa5-722f-4ac4-b734-2131ff86cb68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:01:45,118] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:01:45,118] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:01:45,118] [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	77.3405	218	1307	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.265	222	1307	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	77.1484	196	1307	95	below_threshold
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	76.6675	135	1307	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	76.646	97	1307	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	76.5169	136	1307	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	76.4254	82	1307	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	76.4037	83	1307	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	76.4032	89	1307	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	76.3792	108	1307	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.3719	94	1307	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	76.0041	94	1307	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	75.974	55	1307	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	75.9502	60	1307	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	75.8121	94	1307	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	75.7822	56	1307	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	75.7625	71	1307	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	75.7595	63	1307	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:01:45,118] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11344/tc_result.tsv
[2023-03-17 05:01:45,118] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:01:45,119] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:01:45,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cc6faa5-722f-4ac4-b734-2131ff86cb68/dqc_reference/checkm_data
[2023-03-17 05:01:45,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:01:45,135] [INFO] Task started: CheckM
[2023-03-17 05:01:45,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11344/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11344/checkm_input OceanDNA-b11344/checkm_result
[2023-03-17 05:02:48,137] [INFO] Task succeeded: CheckM
[2023-03-17 05:02:48,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:02:48,140] [INFO] ===== Completeness check finished =====
[2023-03-17 05:02:48,140] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:02:48,140] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11344/markers.fasta)
[2023-03-17 05:02:48,141] [INFO] Task started: Blastn
[2023-03-17 05:02:48,141] [INFO] Running command: blastn -query OceanDNA-b11344/markers.fasta -db /var/lib/cwl/stg4cc6faa5-722f-4ac4-b734-2131ff86cb68/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11344/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:02:48,962] [INFO] Task succeeded: Blastn
[2023-03-17 05:02:48,963] [INFO] Selected 26 target genomes.
[2023-03-17 05:02:48,963] [INFO] Target genome list was writen to OceanDNA-b11344/target_genomes_gtdb.txt
[2023-03-17 05:02:49,280] [INFO] Task started: fastANI
[2023-03-17 05:02:49,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg2807d4d7-bf70-42fb-a670-dd9971049d57/OceanDNA-b11344.fa --refList OceanDNA-b11344/target_genomes_gtdb.txt --output OceanDNA-b11344/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:03:02,868] [INFO] Task succeeded: fastANI
[2023-03-17 05:03:02,881] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:03:02,881] [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	77.3428	217	1307	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	77.1611	195	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425305.1	s__Psychroserpens burtonensis	76.973	87	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	76.7708	114	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900489465.1	s__Aequorivita sp900489465	76.7432	95	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009014635.1	s__Patiriisocius marinistellae	76.6685	136	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018669795.1	s__GCA-002733185 sp018669795	76.6134	122	1307	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_008974325.1	s__Patiriisocius marinus	76.5321	135	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713705.1	s__GCA-002733185 sp002713705	76.5068	93	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	97.32	97.11	0.93	0.92	3	-
GCF_016864015.1	s__Oceanihabitans sp016864015	76.378	104	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997135.1	s__Aequorivita lipolytica	76.3749	107	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018067265.1	s__Oceanihabitans sp018067265	76.2985	65	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831645.1	s__Olleya sp002831645	76.2424	70	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346335.1	s__Aequorivita sinensis	76.1665	94	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCA_002364245.1	s__Marixanthomonas sp002364245	76.1496	60	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	76.0883	73	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694465.1	s__IN17 sp002694465	76.0553	105	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
GCF_003148645.1	s__Xanthomarina spongicola	75.9684	88	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366675.1	s__Xanthomarina sp002366675	75.9625	62	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086205.1	s__Algorimicrobium myxarmorum	75.9502	60	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086165.1	s__Algorimicrobium algoritergicola	75.8266	93	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_003650305.1	s__PRS1 sp003650305	75.7156	76	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667275.1	s__Mesonia aquimarina	75.5269	58	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:03:02,881] [INFO] GTDB search result was written to OceanDNA-b11344/result_gtdb.tsv
[2023-03-17 05:03:02,881] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:03:02,883] [INFO] DFAST_QC result json was written to OceanDNA-b11344/dqc_result.json
[2023-03-17 05:03:02,884] [INFO] DFAST_QC completed!
[2023-03-17 05:03:02,884] [INFO] Total running time: 0h1m56s