[2023-03-16 05:50:18,332] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:50:18,332] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:50:18,332] [INFO] DQC Reference Directory: /var/lib/cwl/stgb27239f2-5d44-4d92-a290-87038c0a5bd0/dqc_reference
[2023-03-16 05:50:20,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:50:20,129] [INFO] Task started: Prodigal
[2023-03-16 05:50:20,129] [INFO] Running command: cat /var/lib/cwl/stgb36d2e34-2050-49c4-839a-866f9143d98f/OceanDNA-b7131.fa | prodigal -d OceanDNA-b7131/cds.fna -a OceanDNA-b7131/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:50:37,110] [INFO] Task succeeded: Prodigal
[2023-03-16 05:50:37,110] [INFO] Task started: HMMsearch
[2023-03-16 05:50:37,110] [INFO] Running command: hmmsearch --tblout OceanDNA-b7131/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb27239f2-5d44-4d92-a290-87038c0a5bd0/dqc_reference/reference_markers.hmm OceanDNA-b7131/protein.faa > /dev/null
[2023-03-16 05:50:37,337] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:50:37,337] [INFO] Found 6/6 markers.
[2023-03-16 05:50:37,356] [INFO] Query marker FASTA was written to OceanDNA-b7131/markers.fasta
[2023-03-16 05:50:37,358] [INFO] Task started: Blastn
[2023-03-16 05:50:37,358] [INFO] Running command: blastn -query OceanDNA-b7131/markers.fasta -db /var/lib/cwl/stgb27239f2-5d44-4d92-a290-87038c0a5bd0/dqc_reference/reference_markers.fasta -out OceanDNA-b7131/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:50:37,993] [INFO] Task succeeded: Blastn
[2023-03-16 05:50:37,994] [INFO] Selected 38 target genomes.
[2023-03-16 05:50:37,994] [INFO] Target genome list was writen to OceanDNA-b7131/target_genomes.txt
[2023-03-16 05:50:38,015] [INFO] Task started: fastANI
[2023-03-16 05:50:38,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgb36d2e34-2050-49c4-839a-866f9143d98f/OceanDNA-b7131.fa --refList OceanDNA-b7131/target_genomes.txt --output OceanDNA-b7131/fastani_result.tsv --threads 1
[2023-03-16 05:50:59,229] [INFO] Task succeeded: fastANI
[2023-03-16 05:50:59,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb27239f2-5d44-4d92-a290-87038c0a5bd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:50:59,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb27239f2-5d44-4d92-a290-87038c0a5bd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:50:59,248] [INFO] Found 37 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:50:59,249] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:50:59,249] [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	76.7988	129	892	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.6897	127	892	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	76.6886	90	892	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	76.6093	77	892	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	76.5671	128	892	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.4282	79	892	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.4053	73	892	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	76.3382	122	892	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.2957	94	892	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	76.2469	119	892	95	below_threshold
Formosa agariphila	strain=type strain: KMM 3901	GCA_000723205.1	320324	320324	type	True	76.2356	86	892	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	76.2298	94	892	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	76.2199	84	892	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.1911	101	892	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	76.146	76	892	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.1113	91	892	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.1103	79	892	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	76.0795	84	892	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.066	74	892	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	76.0589	90	892	95	below_threshold
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	76.049	85	892	95	below_threshold
Flavobacterium terrae	strain=DSM 18829	GCA_900142035.1	415425	415425	type	True	76.0072	68	892	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	76.0057	89	892	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	75.9075	113	892	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	75.9068	79	892	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	75.894	95	892	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	75.8414	118	892	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	75.8375	89	892	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	75.8331	124	892	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	75.8123	123	892	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	75.7732	97	892	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	75.7602	79	892	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	75.7601	61	892	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	75.7082	76	892	95	below_threshold
Flavobacterium granuli	strain=DSM 19729	GCA_900129705.1	280093	280093	type	True	75.5163	52	892	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	75.5139	83	892	95	below_threshold
Flavobacterium granuli	strain=DSM 17797	GCA_003003155.1	280093	280093	type	True	75.502	53	892	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:50:59,249] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7131/tc_result.tsv
[2023-03-16 05:50:59,249] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:50:59,249] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:50:59,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb27239f2-5d44-4d92-a290-87038c0a5bd0/dqc_reference/checkm_data
[2023-03-16 05:50:59,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:50:59,578] [INFO] Task started: CheckM
[2023-03-16 05:50:59,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7131/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7131/checkm_input OceanDNA-b7131/checkm_result
[2023-03-16 05:51:42,920] [INFO] Task succeeded: CheckM
[2023-03-16 05:51:42,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 05:51:42,923] [INFO] ===== Completeness check finished =====
[2023-03-16 05:51:42,923] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:51:42,923] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7131/markers.fasta)
[2023-03-16 05:51:42,924] [INFO] Task started: Blastn
[2023-03-16 05:51:42,925] [INFO] Running command: blastn -query OceanDNA-b7131/markers.fasta -db /var/lib/cwl/stgb27239f2-5d44-4d92-a290-87038c0a5bd0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7131/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:51:43,827] [INFO] Task succeeded: Blastn
[2023-03-16 05:51:43,829] [INFO] Selected 23 target genomes.
[2023-03-16 05:51:43,829] [INFO] Target genome list was writen to OceanDNA-b7131/target_genomes_gtdb.txt
[2023-03-16 05:51:43,848] [INFO] Task started: fastANI
[2023-03-16 05:51:43,848] [INFO] Running command: fastANI --query /var/lib/cwl/stgb36d2e34-2050-49c4-839a-866f9143d98f/OceanDNA-b7131.fa --refList OceanDNA-b7131/target_genomes_gtdb.txt --output OceanDNA-b7131/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:51:58,571] [INFO] Task succeeded: fastANI
[2023-03-16 05:51:58,584] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:51:58,584] [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_013214625.1	s__GCA-2733415 sp013214625	99.5318	758	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2733415	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002733415.1	s__GCA-2733415 sp002733415	94.1835	738	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2733415	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418085.1	s__Lacinutrix algicola	76.5671	128	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	76.5525	116	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518485.1	s__Olleya marilimosa	76.3382	122	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_900114265.1	s__Flaviramulus basaltis	76.3373	108	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	76.3363	94	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	76.313	111	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	76.2725	125	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000723205.1	s__Formosa agariphila	76.2356	86	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009901525.1	s__Kordia antarctica	76.2298	94	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	76.1911	101	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	76.1803	120	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139515.1	s__Lutibacter sp013139515	76.0739	74	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861125.1	s__Cellulophaga baltica_A	76.0561	87	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	75.9367	98	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	75.9316	111	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	75.9142	95	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	75.9068	79	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634105.1	s__Maribacter_B vaceletii	75.894	95	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	75.8538	122	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_008370685.1	s__Aquimarina sp008370685	75.6511	77	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111025.1	s__Jejuia jejuensis	75.6079	75	892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:51:58,584] [INFO] GTDB search result was written to OceanDNA-b7131/result_gtdb.tsv
[2023-03-16 05:51:58,584] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:51:58,587] [INFO] DFAST_QC result json was written to OceanDNA-b7131/dqc_result.json
[2023-03-16 05:51:58,587] [INFO] DFAST_QC completed!
[2023-03-16 05:51:58,587] [INFO] Total running time: 0h1m40s