[2023-03-18 09:41:07,189] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,189] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,190] [INFO] DQC Reference Directory: /var/lib/cwl/stgb06bda2a-98c8-4056-989f-e369855f03f7/dqc_reference
[2023-03-18 09:41:08,271] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:08,272] [INFO] Task started: Prodigal
[2023-03-18 09:41:08,272] [INFO] Running command: cat /var/lib/cwl/stg2c1b3847-4a4a-4a40-b079-2b181e1199bf/OceanDNA-b11427.fa | prodigal -d OceanDNA-b11427/cds.fna -a OceanDNA-b11427/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:26,867] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:26,867] [INFO] Task started: HMMsearch
[2023-03-18 09:41:26,867] [INFO] Running command: hmmsearch --tblout OceanDNA-b11427/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb06bda2a-98c8-4056-989f-e369855f03f7/dqc_reference/reference_markers.hmm OceanDNA-b11427/protein.faa > /dev/null
[2023-03-18 09:41:27,100] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:27,101] [INFO] Found 6/6 markers.
[2023-03-18 09:41:27,123] [INFO] Query marker FASTA was written to OceanDNA-b11427/markers.fasta
[2023-03-18 09:41:27,123] [INFO] Task started: Blastn
[2023-03-18 09:41:27,123] [INFO] Running command: blastn -query OceanDNA-b11427/markers.fasta -db /var/lib/cwl/stgb06bda2a-98c8-4056-989f-e369855f03f7/dqc_reference/reference_markers.fasta -out OceanDNA-b11427/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:27,775] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:27,775] [INFO] Selected 19 target genomes.
[2023-03-18 09:41:27,776] [INFO] Target genome list was writen to OceanDNA-b11427/target_genomes.txt
[2023-03-18 09:41:27,786] [INFO] Task started: fastANI
[2023-03-18 09:41:27,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c1b3847-4a4a-4a40-b079-2b181e1199bf/OceanDNA-b11427.fa --refList OceanDNA-b11427/target_genomes.txt --output OceanDNA-b11427/fastani_result.tsv --threads 1
[2023-03-18 09:41:42,321] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:42,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb06bda2a-98c8-4056-989f-e369855f03f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:42,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb06bda2a-98c8-4056-989f-e369855f03f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:42,332] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:42,332] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:41:42,332] [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 algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	86.4528	673	916	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	79.0403	436	916	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	79.0355	437	916	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	78.6492	417	916	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.5939	388	916	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.4704	340	916	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.4431	386	916	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	78.3758	334	916	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	78.3505	368	916	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	78.3155	351	916	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	78.3118	346	916	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	78.3071	345	916	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	77.9556	332	916	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.7529	231	916	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.6437	177	916	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.2763	189	916	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.1546	202	916	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.0087	126	916	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.8192	137	916	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:41:42,332] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11427/tc_result.tsv
[2023-03-18 09:41:42,333] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:42,333] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:42,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb06bda2a-98c8-4056-989f-e369855f03f7/dqc_reference/checkm_data
[2023-03-18 09:41:42,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:42,339] [INFO] Task started: CheckM
[2023-03-18 09:41:42,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11427/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11427/checkm_input OceanDNA-b11427/checkm_result
[2023-03-18 09:42:29,493] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:29,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.81%
Contamintation: 4.26%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:29,496] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:29,497] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:29,497] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11427/markers.fasta)
[2023-03-18 09:42:29,497] [INFO] Task started: Blastn
[2023-03-18 09:42:29,497] [INFO] Running command: blastn -query OceanDNA-b11427/markers.fasta -db /var/lib/cwl/stgb06bda2a-98c8-4056-989f-e369855f03f7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11427/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:30,398] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:30,399] [INFO] Selected 15 target genomes.
[2023-03-18 09:42:30,399] [INFO] Target genome list was writen to OceanDNA-b11427/target_genomes_gtdb.txt
[2023-03-18 09:42:30,413] [INFO] Task started: fastANI
[2023-03-18 09:42:30,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c1b3847-4a4a-4a40-b079-2b181e1199bf/OceanDNA-b11427.fa --refList OceanDNA-b11427/target_genomes_gtdb.txt --output OceanDNA-b11427/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:40,581] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:40,590] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:42:40,590] [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_002722255.1	s__Winogradskyella sp002722255	99.8104	794	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	conclusive
GCA_002682935.1	s__Winogradskyella sp002682935	86.8763	664	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869935.1	s__Winogradskyella algicola	86.4528	673	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971725.1	s__Winogradskyella sp001971725	84.7326	622	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706045.1	s__Winogradskyella sp002706045	80.5034	327	916	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	79.0353	437	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009709615.1	s__Winogradskyella ouciana	78.6522	417	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCA_000171875.1	s__Winogradskyella sp000171875	78.5979	385	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019203985.1	s__Winogradskyella sp019203985	78.5134	390	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	78.5083	377	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	78.4831	391	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	78.4558	339	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_013249045.1	s__Winogradskyella eckloniae	78.3923	332	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	78.3868	379	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213975.1	s__Winogradskyella sp013213975	78.2912	287	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:40,591] [INFO] GTDB search result was written to OceanDNA-b11427/result_gtdb.tsv
[2023-03-18 09:42:40,591] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:40,593] [INFO] DFAST_QC result json was written to OceanDNA-b11427/dqc_result.json
[2023-03-18 09:42:40,593] [INFO] DFAST_QC completed!
[2023-03-18 09:42:40,593] [INFO] Total running time: 0h1m33s