[2023-03-14 12:49:51,922] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:49:51,922] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:49:51,923] [INFO] DQC Reference Directory: /var/lib/cwl/stgf03710a6-293b-41f1-94d5-49bdab0d91b2/dqc_reference
[2023-03-14 12:49:53,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:49:53,357] [INFO] Task started: Prodigal
[2023-03-14 12:49:53,357] [INFO] Running command: cat /var/lib/cwl/stgee4408aa-e772-4e29-bf61-a0c914a1221c/OceanDNA-b7391.fa | prodigal -d OceanDNA-b7391/cds.fna -a OceanDNA-b7391/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:50:07,830] [INFO] Task succeeded: Prodigal
[2023-03-14 12:50:07,831] [INFO] Task started: HMMsearch
[2023-03-14 12:50:07,831] [INFO] Running command: hmmsearch --tblout OceanDNA-b7391/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf03710a6-293b-41f1-94d5-49bdab0d91b2/dqc_reference/reference_markers.hmm OceanDNA-b7391/protein.faa > /dev/null
[2023-03-14 12:50:08,160] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:50:08,161] [INFO] Found 6/6 markers.
[2023-03-14 12:50:08,177] [INFO] Query marker FASTA was written to OceanDNA-b7391/markers.fasta
[2023-03-14 12:50:08,178] [INFO] Task started: Blastn
[2023-03-14 12:50:08,178] [INFO] Running command: blastn -query OceanDNA-b7391/markers.fasta -db /var/lib/cwl/stgf03710a6-293b-41f1-94d5-49bdab0d91b2/dqc_reference/reference_markers.fasta -out OceanDNA-b7391/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:50:08,963] [INFO] Task succeeded: Blastn
[2023-03-14 12:50:08,964] [INFO] Selected 30 target genomes.
[2023-03-14 12:50:08,964] [INFO] Target genome list was writen to OceanDNA-b7391/target_genomes.txt
[2023-03-14 12:50:08,986] [INFO] Task started: fastANI
[2023-03-14 12:50:08,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgee4408aa-e772-4e29-bf61-a0c914a1221c/OceanDNA-b7391.fa --refList OceanDNA-b7391/target_genomes.txt --output OceanDNA-b7391/fastani_result.tsv --threads 1
[2023-03-14 12:50:25,599] [INFO] Task succeeded: fastANI
[2023-03-14 12:50:25,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf03710a6-293b-41f1-94d5-49bdab0d91b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:50:25,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf03710a6-293b-41f1-94d5-49bdab0d91b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:50:25,614] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:50:25,615] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:50:25,615] [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
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.6676	83	630	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	76.5474	68	630	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.4924	69	630	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	76.4084	67	630	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.399	85	630	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	76.3921	87	630	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	76.3678	83	630	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.3655	93	630	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.3173	98	630	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	76.275	67	630	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.2596	63	630	95	below_threshold
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	76.2544	57	630	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.2421	88	630	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.2421	88	630	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.2012	62	630	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.2003	92	630	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.1984	75	630	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.1752	78	630	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	76.1219	63	630	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	76.1214	79	630	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.1122	93	630	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	75.9946	75	630	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	75.9611	75	630	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	75.9562	73	630	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	75.9384	72	630	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	75.8402	66	630	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	75.8275	62	630	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:50:25,615] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7391/tc_result.tsv
[2023-03-14 12:50:25,615] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:50:25,615] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:50:25,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf03710a6-293b-41f1-94d5-49bdab0d91b2/dqc_reference/checkm_data
[2023-03-14 12:50:25,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:50:25,641] [INFO] Task started: CheckM
[2023-03-14 12:50:25,641] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7391/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7391/checkm_input OceanDNA-b7391/checkm_result
[2023-03-14 12:51:04,849] [INFO] Task succeeded: CheckM
[2023-03-14 12:51:04,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.99%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:51:04,853] [INFO] ===== Completeness check finished =====
[2023-03-14 12:51:04,854] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:51:04,854] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7391/markers.fasta)
[2023-03-14 12:51:04,855] [INFO] Task started: Blastn
[2023-03-14 12:51:04,855] [INFO] Running command: blastn -query OceanDNA-b7391/markers.fasta -db /var/lib/cwl/stgf03710a6-293b-41f1-94d5-49bdab0d91b2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7391/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:51:07,111] [INFO] Task succeeded: Blastn
[2023-03-14 12:51:07,113] [INFO] Selected 9 target genomes.
[2023-03-14 12:51:07,113] [INFO] Target genome list was writen to OceanDNA-b7391/target_genomes_gtdb.txt
[2023-03-14 12:51:07,124] [INFO] Task started: fastANI
[2023-03-14 12:51:07,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgee4408aa-e772-4e29-bf61-a0c914a1221c/OceanDNA-b7391.fa --refList OceanDNA-b7391/target_genomes_gtdb.txt --output OceanDNA-b7391/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:51:15,317] [INFO] Task succeeded: fastANI
[2023-03-14 12:51:15,323] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:51:15,323] [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_905181825.1	s__Hel1-33-131 sp905181825	99.4311	472	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	conclusive
GCA_018608625.1	s__Hel1-33-131 sp018608625	84.1464	462	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCA_018608705.1	s__Hel1-33-131 sp018608705	80.4917	376	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.44	99.44	0.94	0.94	2	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	79.641	319	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	79.2459	285	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	79.0949	310	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608735.1	s__Hel1-33-131 sp018608735	78.8654	212	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	78.8604	276	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	78.8085	277	630	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:51:15,324] [INFO] GTDB search result was written to OceanDNA-b7391/result_gtdb.tsv
[2023-03-14 12:51:15,324] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:51:15,327] [INFO] DFAST_QC result json was written to OceanDNA-b7391/dqc_result.json
[2023-03-14 12:51:15,327] [INFO] DFAST_QC completed!
[2023-03-14 12:51:15,327] [INFO] Total running time: 0h1m23s