[2023-03-17 05:01:06,443] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:01:06,443] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:01:06,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg0552f493-6db6-44e4-a8e4-2b1013093edd/dqc_reference
[2023-03-17 05:01:07,999] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:01:07,999] [INFO] Task started: Prodigal
[2023-03-17 05:01:08,000] [INFO] Running command: cat /var/lib/cwl/stg479fee92-ec81-4563-b91f-09b49e5da32a/OceanDNA-b6256.fa | prodigal -d OceanDNA-b6256/cds.fna -a OceanDNA-b6256/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:01:20,581] [INFO] Task succeeded: Prodigal
[2023-03-17 05:01:20,581] [INFO] Task started: HMMsearch
[2023-03-17 05:01:20,581] [INFO] Running command: hmmsearch --tblout OceanDNA-b6256/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0552f493-6db6-44e4-a8e4-2b1013093edd/dqc_reference/reference_markers.hmm OceanDNA-b6256/protein.faa > /dev/null
[2023-03-17 05:01:20,767] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:01:20,767] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg479fee92-ec81-4563-b91f-09b49e5da32a/OceanDNA-b6256.fa]
[2023-03-17 05:01:20,782] [INFO] Query marker FASTA was written to OceanDNA-b6256/markers.fasta
[2023-03-17 05:01:20,783] [INFO] Task started: Blastn
[2023-03-17 05:01:20,783] [INFO] Running command: blastn -query OceanDNA-b6256/markers.fasta -db /var/lib/cwl/stg0552f493-6db6-44e4-a8e4-2b1013093edd/dqc_reference/reference_markers.fasta -out OceanDNA-b6256/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:01:21,331] [INFO] Task succeeded: Blastn
[2023-03-17 05:01:21,332] [INFO] Selected 22 target genomes.
[2023-03-17 05:01:21,332] [INFO] Target genome list was writen to OceanDNA-b6256/target_genomes.txt
[2023-03-17 05:01:21,341] [INFO] Task started: fastANI
[2023-03-17 05:01:21,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg479fee92-ec81-4563-b91f-09b49e5da32a/OceanDNA-b6256.fa --refList OceanDNA-b6256/target_genomes.txt --output OceanDNA-b6256/fastani_result.tsv --threads 1
[2023-03-17 05:01:34,681] [INFO] Task succeeded: fastANI
[2023-03-17 05:01:34,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0552f493-6db6-44e4-a8e4-2b1013093edd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:01:34,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0552f493-6db6-44e4-a8e4-2b1013093edd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:01:34,693] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:01:34,693] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:01:34,694] [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
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.749	122	672	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	76.645	82	672	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.5786	126	672	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.5693	94	672	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	76.5668	104	672	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.5382	84	672	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.4993	131	672	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	76.4905	118	672	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.4722	104	672	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.472	117	672	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.4077	89	672	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.3414	89	672	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.3347	136	672	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	76.2857	96	672	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	76.246	102	672	95	below_threshold
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	76.2013	72	672	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.1509	94	672	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.1358	58	672	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	75.8417	85	672	95	below_threshold
Aquimarina algicola	strain=M625	GCA_006443095.1	2589995	2589995	type	True	75.7515	62	672	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	75.623	58	672	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:01:34,694] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6256/tc_result.tsv
[2023-03-17 05:01:34,694] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:01:34,694] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:01:34,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0552f493-6db6-44e4-a8e4-2b1013093edd/dqc_reference/checkm_data
[2023-03-17 05:01:34,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:01:34,698] [INFO] Task started: CheckM
[2023-03-17 05:01:34,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6256/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6256/checkm_input OceanDNA-b6256/checkm_result
[2023-03-17 05:02:09,569] [INFO] Task succeeded: CheckM
[2023-03-17 05:02:09,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.37%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:02:09,571] [INFO] ===== Completeness check finished =====
[2023-03-17 05:02:09,571] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:02:09,571] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6256/markers.fasta)
[2023-03-17 05:02:09,572] [INFO] Task started: Blastn
[2023-03-17 05:02:09,572] [INFO] Running command: blastn -query OceanDNA-b6256/markers.fasta -db /var/lib/cwl/stg0552f493-6db6-44e4-a8e4-2b1013093edd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6256/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:02:10,316] [INFO] Task succeeded: Blastn
[2023-03-17 05:02:10,317] [INFO] Selected 22 target genomes.
[2023-03-17 05:02:10,317] [INFO] Target genome list was writen to OceanDNA-b6256/target_genomes_gtdb.txt
[2023-03-17 05:02:10,765] [INFO] Task started: fastANI
[2023-03-17 05:02:10,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg479fee92-ec81-4563-b91f-09b49e5da32a/OceanDNA-b6256.fa --refList OceanDNA-b6256/target_genomes_gtdb.txt --output OceanDNA-b6256/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:02:22,838] [INFO] Task succeeded: fastANI
[2023-03-17 05:02:22,850] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:02:22,850] [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_003650305.1	s__PRS1 sp003650305	76.8713	106	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148645.1	s__Xanthomarina spongicola	76.7256	115	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	76.7187	122	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722255.1	s__Winogradskyella sp002722255	76.6647	110	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_002163855.1	s__Winogradskyella sp002163855	76.6261	93	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.88	99.82	0.99	0.99	3	-
GCF_003386165.1	s__Winogradskyella eximia	76.5495	125	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047595.1	s__CAU-1491 sp005047595	76.4855	130	672	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_013403925.1	s__Winogradskyella wichelsiae	76.4705	117	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	76.4307	127	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	76.362	120	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366675.1	s__Xanthomarina sp002366675	76.3567	97	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	76.3294	135	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785945.1	s__Olleya sediminilitoris	76.3251	105	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	-
GCA_905480385.1	s__Winogradskyella sp905480385	76.3193	75	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.53	99.53	0.86	0.86	2	-
GCA_018222875.1	s__Psychroserpens sp018222875	76.2468	100	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430645.1	s__Aquimarina latercula	76.2299	73	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.44	98.41	0.94	0.92	4	-
GCF_014202195.1	s__Oceanihabitans iliipiscarium	76.1962	104	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	76.1323	95	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCA_001874335.1	s__MedPE-SWsnd-G2 sp001874335	76.1246	95	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MedPE-SWsnd-G2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238425.1	s__JABABD01 sp014238425	76.0958	86	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__JABABD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006443095.1	s__Aquimarina sp006443095	75.7515	62	672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:02:22,851] [INFO] GTDB search result was written to OceanDNA-b6256/result_gtdb.tsv
[2023-03-17 05:02:22,851] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:02:22,853] [INFO] DFAST_QC result json was written to OceanDNA-b6256/dqc_result.json
[2023-03-17 05:02:22,853] [INFO] DFAST_QC completed!
[2023-03-17 05:02:22,853] [INFO] Total running time: 0h1m16s