[2023-03-15 21:16:33,623] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:16:33,623] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:16:33,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bf65803-0b2c-4872-9552-719c6b3317e9/dqc_reference
[2023-03-15 21:16:35,476] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:16:35,476] [INFO] Task started: Prodigal
[2023-03-15 21:16:35,476] [INFO] Running command: cat /var/lib/cwl/stgefe1d4d6-c7ad-487b-b691-5fedfb2004ed/OceanDNA-b6251.fa | prodigal -d OceanDNA-b6251/cds.fna -a OceanDNA-b6251/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:16:51,087] [INFO] Task succeeded: Prodigal
[2023-03-15 21:16:51,088] [INFO] Task started: HMMsearch
[2023-03-15 21:16:51,088] [INFO] Running command: hmmsearch --tblout OceanDNA-b6251/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bf65803-0b2c-4872-9552-719c6b3317e9/dqc_reference/reference_markers.hmm OceanDNA-b6251/protein.faa > /dev/null
[2023-03-15 21:16:51,278] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:16:51,279] [INFO] Found 6/6 markers.
[2023-03-15 21:16:51,294] [INFO] Query marker FASTA was written to OceanDNA-b6251/markers.fasta
[2023-03-15 21:16:51,295] [INFO] Task started: Blastn
[2023-03-15 21:16:51,295] [INFO] Running command: blastn -query OceanDNA-b6251/markers.fasta -db /var/lib/cwl/stg3bf65803-0b2c-4872-9552-719c6b3317e9/dqc_reference/reference_markers.fasta -out OceanDNA-b6251/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:16:51,857] [INFO] Task succeeded: Blastn
[2023-03-15 21:16:51,858] [INFO] Selected 32 target genomes.
[2023-03-15 21:16:51,858] [INFO] Target genome list was writen to OceanDNA-b6251/target_genomes.txt
[2023-03-15 21:16:51,879] [INFO] Task started: fastANI
[2023-03-15 21:16:51,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgefe1d4d6-c7ad-487b-b691-5fedfb2004ed/OceanDNA-b6251.fa --refList OceanDNA-b6251/target_genomes.txt --output OceanDNA-b6251/fastani_result.tsv --threads 1
[2023-03-15 21:17:09,495] [INFO] Task succeeded: fastANI
[2023-03-15 21:17:09,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bf65803-0b2c-4872-9552-719c6b3317e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:17:09,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bf65803-0b2c-4872-9552-719c6b3317e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:17:09,512] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:17:09,512] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:17:09,512] [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
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.0542	176	784	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.8234	103	784	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	76.8041	104	784	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.7816	106	784	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.7808	93	784	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.76	107	784	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.7577	138	784	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.7577	138	784	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.6491	90	784	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.6395	100	784	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	76.6214	113	784	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	76.6122	91	784	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	76.6046	109	784	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	76.5887	95	784	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	76.5656	101	784	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.5343	101	784	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	76.4899	122	784	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.4732	109	784	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	76.4725	93	784	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.4584	89	784	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.4579	104	784	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.4535	119	784	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.4525	93	784	95	below_threshold
Aestuariivivens sediminis	strain=S-DT1-15	GCA_022662105.1	2913557	2913557	type	True	76.4377	76	784	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	76.3862	77	784	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	76.3727	94	784	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.3363	116	784	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.2926	110	784	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	75.916	67	784	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:17:09,512] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6251/tc_result.tsv
[2023-03-15 21:17:09,512] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:17:09,513] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:17:09,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bf65803-0b2c-4872-9552-719c6b3317e9/dqc_reference/checkm_data
[2023-03-15 21:17:09,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:17:09,678] [INFO] Task started: CheckM
[2023-03-15 21:17:09,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6251/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6251/checkm_input OceanDNA-b6251/checkm_result
[2023-03-15 21:17:51,676] [INFO] Task succeeded: CheckM
[2023-03-15 21:17:51,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:17:51,678] [INFO] ===== Completeness check finished =====
[2023-03-15 21:17:51,678] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:17:51,679] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6251/markers.fasta)
[2023-03-15 21:17:51,680] [INFO] Task started: Blastn
[2023-03-15 21:17:51,680] [INFO] Running command: blastn -query OceanDNA-b6251/markers.fasta -db /var/lib/cwl/stg3bf65803-0b2c-4872-9552-719c6b3317e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6251/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:17:52,478] [INFO] Task succeeded: Blastn
[2023-03-15 21:17:52,479] [INFO] Selected 28 target genomes.
[2023-03-15 21:17:52,479] [INFO] Target genome list was writen to OceanDNA-b6251/target_genomes_gtdb.txt
[2023-03-15 21:17:52,896] [INFO] Task started: fastANI
[2023-03-15 21:17:52,896] [INFO] Running command: fastANI --query /var/lib/cwl/stgefe1d4d6-c7ad-487b-b691-5fedfb2004ed/OceanDNA-b6251.fa --refList OceanDNA-b6251/target_genomes_gtdb.txt --output OceanDNA-b6251/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:18:08,260] [INFO] Task succeeded: fastANI
[2023-03-15 21:18:08,275] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:18:08,276] [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_905479065.1	s__CAJQLB01 sp905479065	99.7748	737	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAJQLB01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011777505.1	s__CAU-1491 sp011777505	77.2848	161	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	77.1718	114	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047595.1	s__CAU-1491 sp005047595	77.0691	175	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148645.1	s__Xanthomarina spongicola	76.9272	123	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	76.8041	104	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	76.7507	117	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	76.7449	135	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	76.7313	105	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003144015.1	s__Xanthomarina sp003144015	76.707	118	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	76.6957	127	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	76.6822	139	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258355.1	s__Confluentibacter sp003258355	76.6122	91	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944795.1	s__Mangrovimonas spongiae	76.6116	94	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414705.1	s__Algorimicrobium sp002414705	76.5988	106	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014526325.1	s__Psychroserpens algicola	76.5986	117	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	76.5441	128	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	76.5241	113	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	76.5112	120	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	76.4732	109	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162765.1	s__MAAR01 sp002162765	76.4598	108	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	76.4584	89	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_013404085.1	s__Winogradskyella helgolandensis	76.4525	93	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_004346845.1	s__Winogradskyella wandonensis	76.4118	76	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129745.1	s__Winogradskyella jejuensis	76.3936	93	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	76.2587	81	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479815.1	s__Psychroserpens sp905479815	75.704	99	784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:18:08,276] [INFO] GTDB search result was written to OceanDNA-b6251/result_gtdb.tsv
[2023-03-15 21:18:08,276] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:18:08,279] [INFO] DFAST_QC result json was written to OceanDNA-b6251/dqc_result.json
[2023-03-15 21:18:08,279] [INFO] DFAST_QC completed!
[2023-03-15 21:18:08,279] [INFO] Total running time: 0h1m35s