[2023-03-16 09:06:46,779] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:06:46,779] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:06:46,779] [INFO] DQC Reference Directory: /var/lib/cwl/stg070bb455-6550-426f-8659-260948e25ffe/dqc_reference
[2023-03-16 09:06:47,894] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:06:47,895] [INFO] Task started: Prodigal
[2023-03-16 09:06:47,895] [INFO] Running command: cat /var/lib/cwl/stg019409c8-9fea-4d6a-b102-cbb0a77c29e9/OceanDNA-b11421.fa | prodigal -d OceanDNA-b11421/cds.fna -a OceanDNA-b11421/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:07:09,498] [INFO] Task succeeded: Prodigal
[2023-03-16 09:07:09,499] [INFO] Task started: HMMsearch
[2023-03-16 09:07:09,499] [INFO] Running command: hmmsearch --tblout OceanDNA-b11421/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg070bb455-6550-426f-8659-260948e25ffe/dqc_reference/reference_markers.hmm OceanDNA-b11421/protein.faa > /dev/null
[2023-03-16 09:07:09,717] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:07:09,718] [INFO] Found 6/6 markers.
[2023-03-16 09:07:09,739] [INFO] Query marker FASTA was written to OceanDNA-b11421/markers.fasta
[2023-03-16 09:07:09,740] [INFO] Task started: Blastn
[2023-03-16 09:07:09,740] [INFO] Running command: blastn -query OceanDNA-b11421/markers.fasta -db /var/lib/cwl/stg070bb455-6550-426f-8659-260948e25ffe/dqc_reference/reference_markers.fasta -out OceanDNA-b11421/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:07:10,379] [INFO] Task succeeded: Blastn
[2023-03-16 09:07:10,380] [INFO] Selected 17 target genomes.
[2023-03-16 09:07:10,380] [INFO] Target genome list was writen to OceanDNA-b11421/target_genomes.txt
[2023-03-16 09:07:10,440] [INFO] Task started: fastANI
[2023-03-16 09:07:10,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg019409c8-9fea-4d6a-b102-cbb0a77c29e9/OceanDNA-b11421.fa --refList OceanDNA-b11421/target_genomes.txt --output OceanDNA-b11421/fastani_result.tsv --threads 1
[2023-03-16 09:07:22,219] [INFO] Task succeeded: fastANI
[2023-03-16 09:07:22,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg070bb455-6550-426f-8659-260948e25ffe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:07:22,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg070bb455-6550-426f-8659-260948e25ffe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:07:22,230] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:07:22,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:07:22,230] [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	84.6492	800	1145	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	79.1689	524	1145	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	79.0133	532	1145	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	79.0133	532	1145	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.8611	450	1145	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	78.509	463	1145	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	78.4608	425	1145	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.4456	498	1145	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.3753	433	1145	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	78.3711	450	1145	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	78.3585	419	1145	95	below_threshold
Winogradskyella forsetii	strain=HL857	GCA_013394595.1	2686077	2686077	type	True	78.0589	408	1145	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.267	298	1145	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.2614	198	1145	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.1759	244	1145	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.9793	181	1145	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.664	182	1145	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:07:22,232] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11421/tc_result.tsv
[2023-03-16 09:07:22,234] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:07:22,234] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:07:22,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg070bb455-6550-426f-8659-260948e25ffe/dqc_reference/checkm_data
[2023-03-16 09:07:22,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:07:22,244] [INFO] Task started: CheckM
[2023-03-16 09:07:22,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11421/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11421/checkm_input OceanDNA-b11421/checkm_result
[2023-03-16 09:08:16,789] [INFO] Task succeeded: CheckM
[2023-03-16 09:08:16,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:08:16,808] [INFO] ===== Completeness check finished =====
[2023-03-16 09:08:16,808] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:08:16,808] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11421/markers.fasta)
[2023-03-16 09:08:16,810] [INFO] Task started: Blastn
[2023-03-16 09:08:16,810] [INFO] Running command: blastn -query OceanDNA-b11421/markers.fasta -db /var/lib/cwl/stg070bb455-6550-426f-8659-260948e25ffe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11421/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:08:17,717] [INFO] Task succeeded: Blastn
[2023-03-16 09:08:17,721] [INFO] Selected 13 target genomes.
[2023-03-16 09:08:17,721] [INFO] Target genome list was writen to OceanDNA-b11421/target_genomes_gtdb.txt
[2023-03-16 09:08:17,783] [INFO] Task started: fastANI
[2023-03-16 09:08:17,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg019409c8-9fea-4d6a-b102-cbb0a77c29e9/OceanDNA-b11421.fa --refList OceanDNA-b11421/target_genomes_gtdb.txt --output OceanDNA-b11421/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:08:27,490] [INFO] Task succeeded: fastANI
[2023-03-16 09:08:27,498] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:08:27,499] [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_002682935.1	s__Winogradskyella sp002682935	99.8948	1052	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002722255.1	s__Winogradskyella sp002722255	87.212	729	1145	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	84.6492	800	1145	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	83.6831	768	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709615.1	s__Winogradskyella ouciana	79.1598	525	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.22	97.22	0.91	0.91	2	-
GCF_014297365.1	s__Winogradskyella echinorum	79.0133	532	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019203985.1	s__Winogradskyella sp019203985	78.9292	486	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741275.1	s__Winogradskyella endarachnes	78.8561	451	1145	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	78.6423	473	1145	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	78.5968	434	1145	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	78.5142	368	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	78.4375	499	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099995.1	s__Winogradskyella thalassocola	78.3794	449	1145	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:08:27,500] [INFO] GTDB search result was written to OceanDNA-b11421/result_gtdb.tsv
[2023-03-16 09:08:27,502] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:08:27,506] [INFO] DFAST_QC result json was written to OceanDNA-b11421/dqc_result.json
[2023-03-16 09:08:27,506] [INFO] DFAST_QC completed!
[2023-03-16 09:08:27,506] [INFO] Total running time: 0h1m41s