[2023-03-15 04:37:12,306] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:37:12,306] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:37:12,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg0116f39f-870f-4c14-8e7c-dd4068054a4c/dqc_reference
[2023-03-15 04:37:13,418] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:37:13,418] [INFO] Task started: Prodigal
[2023-03-15 04:37:13,418] [INFO] Running command: cat /var/lib/cwl/stg97262d33-3070-4e19-adb6-330d53912f53/OceanDNA-b11413.fa | prodigal -d OceanDNA-b11413/cds.fna -a OceanDNA-b11413/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:37:23,966] [INFO] Task succeeded: Prodigal
[2023-03-15 04:37:23,966] [INFO] Task started: HMMsearch
[2023-03-15 04:37:23,966] [INFO] Running command: hmmsearch --tblout OceanDNA-b11413/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0116f39f-870f-4c14-8e7c-dd4068054a4c/dqc_reference/reference_markers.hmm OceanDNA-b11413/protein.faa > /dev/null
[2023-03-15 04:37:24,130] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:37:24,131] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg97262d33-3070-4e19-adb6-330d53912f53/OceanDNA-b11413.fa]
[2023-03-15 04:37:24,166] [INFO] Query marker FASTA was written to OceanDNA-b11413/markers.fasta
[2023-03-15 04:37:24,167] [INFO] Task started: Blastn
[2023-03-15 04:37:24,167] [INFO] Running command: blastn -query OceanDNA-b11413/markers.fasta -db /var/lib/cwl/stg0116f39f-870f-4c14-8e7c-dd4068054a4c/dqc_reference/reference_markers.fasta -out OceanDNA-b11413/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:37:24,725] [INFO] Task succeeded: Blastn
[2023-03-15 04:37:24,729] [INFO] Selected 18 target genomes.
[2023-03-15 04:37:24,729] [INFO] Target genome list was writen to OceanDNA-b11413/target_genomes.txt
[2023-03-15 04:37:24,740] [INFO] Task started: fastANI
[2023-03-15 04:37:24,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg97262d33-3070-4e19-adb6-330d53912f53/OceanDNA-b11413.fa --refList OceanDNA-b11413/target_genomes.txt --output OceanDNA-b11413/fastani_result.tsv --threads 1
[2023-03-15 04:37:36,710] [INFO] Task succeeded: fastANI
[2023-03-15 04:37:36,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0116f39f-870f-4c14-8e7c-dd4068054a4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:37:36,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0116f39f-870f-4c14-8e7c-dd4068054a4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:37:36,722] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:37:36,722] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:37:36,722] [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 echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.1299	242	528	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.1299	242	528	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	77.9824	220	528	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	77.8064	185	528	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	77.7134	229	528	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	77.6466	168	528	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	77.4255	173	528	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.3767	169	528	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.3623	192	528	95	below_threshold
Winogradskyella aurantia	strain=WNB302	GCA_002266855.1	1915063	1915063	type	True	77.2236	167	528	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.1802	123	528	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	77.1607	97	528	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.8817	147	528	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.6561	119	528	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	76.6133	100	528	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.5743	113	528	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	76.5339	87	528	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	76.4434	69	528	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:37:36,725] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11413/tc_result.tsv
[2023-03-15 04:37:36,728] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:37:36,728] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:37:36,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0116f39f-870f-4c14-8e7c-dd4068054a4c/dqc_reference/checkm_data
[2023-03-15 04:37:36,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:37:36,738] [INFO] Task started: CheckM
[2023-03-15 04:37:36,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11413/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11413/checkm_input OceanDNA-b11413/checkm_result
[2023-03-15 04:38:07,540] [INFO] Task succeeded: CheckM
[2023-03-15 04:38:07,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:38:07,697] [INFO] ===== Completeness check finished =====
[2023-03-15 04:38:07,697] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:38:07,697] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11413/markers.fasta)
[2023-03-15 04:38:07,698] [INFO] Task started: Blastn
[2023-03-15 04:38:07,699] [INFO] Running command: blastn -query OceanDNA-b11413/markers.fasta -db /var/lib/cwl/stg0116f39f-870f-4c14-8e7c-dd4068054a4c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11413/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:38:08,472] [INFO] Task succeeded: Blastn
[2023-03-15 04:38:08,493] [INFO] Selected 19 target genomes.
[2023-03-15 04:38:08,493] [INFO] Target genome list was writen to OceanDNA-b11413/target_genomes_gtdb.txt
[2023-03-15 04:38:08,514] [INFO] Task started: fastANI
[2023-03-15 04:38:08,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg97262d33-3070-4e19-adb6-330d53912f53/OceanDNA-b11413.fa --refList OceanDNA-b11413/target_genomes_gtdb.txt --output OceanDNA-b11413/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:38:20,405] [INFO] Task succeeded: fastANI
[2023-03-15 04:38:20,416] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:38:20,416] [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_003335675.1	s__Winogradskyella sp003335675	99.1159	521	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000828715.1	s__Winogradskyella sp000828715	78.1333	250	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	78.1299	242	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000171875.1	s__Winogradskyella sp000171875	78.1288	236	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	78.0607	194	528	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	78.0455	190	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_005869935.1	s__Winogradskyella algicola	77.9514	222	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	77.9233	210	528	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	77.876	229	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243395.1	s__Winogradskyella flava	77.7134	229	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480385.1	s__Winogradskyella sp905480385	77.6764	128	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.53	99.53	0.86	0.86	2	-
GCF_013403865.1	s__Winogradskyella costae	77.6466	168	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	77.496	174	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_013394655.1	s__Winogradskyella schleiferi	77.4429	172	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042245.1	s__Winogradskyella sp013042245	77.4023	133	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.97	99.97	0.95	0.95	2	-
GCF_003387355.1	s__Winogradskyella sediminis	77.3623	192	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	77.1802	123	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414705.1	s__Algorimicrobium sp002414705	76.6632	96	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874145.1	s__Lacinutrix sp001874145	76.6351	112	528	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:38:20,419] [INFO] GTDB search result was written to OceanDNA-b11413/result_gtdb.tsv
[2023-03-15 04:38:20,421] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:38:20,425] [INFO] DFAST_QC result json was written to OceanDNA-b11413/dqc_result.json
[2023-03-15 04:38:20,425] [INFO] DFAST_QC completed!
[2023-03-15 04:38:20,425] [INFO] Total running time: 0h1m8s