[2023-03-17 03:16:26,875] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:16:26,875] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:16:26,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg3399230e-7828-4567-a061-49bd9463e49c/dqc_reference
[2023-03-17 03:16:29,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:16:29,245] [INFO] Task started: Prodigal
[2023-03-17 03:16:29,245] [INFO] Running command: cat /var/lib/cwl/stgc2131bd9-e167-446f-a0c3-b2cda82c664e/OceanDNA-b9981.fa | prodigal -d OceanDNA-b9981/cds.fna -a OceanDNA-b9981/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:16:47,155] [INFO] Task succeeded: Prodigal
[2023-03-17 03:16:47,156] [INFO] Task started: HMMsearch
[2023-03-17 03:16:47,156] [INFO] Running command: hmmsearch --tblout OceanDNA-b9981/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3399230e-7828-4567-a061-49bd9463e49c/dqc_reference/reference_markers.hmm OceanDNA-b9981/protein.faa > /dev/null
[2023-03-17 03:16:47,358] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:16:47,358] [INFO] Found 6/6 markers.
[2023-03-17 03:16:47,377] [INFO] Query marker FASTA was written to OceanDNA-b9981/markers.fasta
[2023-03-17 03:16:47,377] [INFO] Task started: Blastn
[2023-03-17 03:16:47,377] [INFO] Running command: blastn -query OceanDNA-b9981/markers.fasta -db /var/lib/cwl/stg3399230e-7828-4567-a061-49bd9463e49c/dqc_reference/reference_markers.fasta -out OceanDNA-b9981/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:16:48,014] [INFO] Task succeeded: Blastn
[2023-03-17 03:16:48,015] [INFO] Selected 18 target genomes.
[2023-03-17 03:16:48,015] [INFO] Target genome list was writen to OceanDNA-b9981/target_genomes.txt
[2023-03-17 03:16:48,078] [INFO] Task started: fastANI
[2023-03-17 03:16:48,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2131bd9-e167-446f-a0c3-b2cda82c664e/OceanDNA-b9981.fa --refList OceanDNA-b9981/target_genomes.txt --output OceanDNA-b9981/fastani_result.tsv --threads 1
[2023-03-17 03:17:00,426] [INFO] Task succeeded: fastANI
[2023-03-17 03:17:00,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3399230e-7828-4567-a061-49bd9463e49c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:17:00,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3399230e-7828-4567-a061-49bd9463e49c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:17:00,437] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:17:00,437] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:17:00,437] [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
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	82.8895	661	966	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	82.8271	656	966	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	82.8169	656	966	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	81.471	606	966	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	81.3476	605	966	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	81.285	636	966	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	81.27	627	966	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	80.737	562	966	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	80.7354	564	966	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.4351	550	966	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	80.123	504	966	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.9063	500	966	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	79.6276	481	966	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	76.952	59	966	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	76.9076	60	966	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	76.1661	66	966	95	below_threshold
Salegentibacter maritimus	strain=F63223	GCA_016236915.1	2794347	2794347	type	True	75.9123	64	966	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:17:00,437] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9981/tc_result.tsv
[2023-03-17 03:17:00,437] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:17:00,437] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:17:00,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3399230e-7828-4567-a061-49bd9463e49c/dqc_reference/checkm_data
[2023-03-17 03:17:00,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:17:00,442] [INFO] Task started: CheckM
[2023-03-17 03:17:00,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9981/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9981/checkm_input OceanDNA-b9981/checkm_result
[2023-03-17 03:17:46,928] [INFO] Task succeeded: CheckM
[2023-03-17 03:17:46,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 13.02%
Strain heterogeneity: 14.29%
--------------------------------------------------------------------------------
[2023-03-17 03:17:46,934] [INFO] ===== Completeness check finished =====
[2023-03-17 03:17:46,934] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:17:46,934] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9981/markers.fasta)
[2023-03-17 03:17:46,936] [INFO] Task started: Blastn
[2023-03-17 03:17:46,937] [INFO] Running command: blastn -query OceanDNA-b9981/markers.fasta -db /var/lib/cwl/stg3399230e-7828-4567-a061-49bd9463e49c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9981/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:17:47,882] [INFO] Task succeeded: Blastn
[2023-03-17 03:17:47,883] [INFO] Selected 15 target genomes.
[2023-03-17 03:17:47,883] [INFO] Target genome list was writen to OceanDNA-b9981/target_genomes_gtdb.txt
[2023-03-17 03:17:47,918] [INFO] Task started: fastANI
[2023-03-17 03:17:47,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2131bd9-e167-446f-a0c3-b2cda82c664e/OceanDNA-b9981.fa --refList OceanDNA-b9981/target_genomes_gtdb.txt --output OceanDNA-b9981/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:17:59,323] [INFO] Task succeeded: fastANI
[2023-03-17 03:17:59,331] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:17:59,331] [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_001280865.1	s__Polaribacter dokdonensis	82.851	653	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000152945.2	s__Polaribacter sp000152945	82.8484	635	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861005.1	s__Polaribacter vadi_A	81.5747	601	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	81.4301	608	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000687935.1	s__Polaribacter sp000687935	81.2851	640	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	81.2846	636	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002954685.1	s__Polaribacter porphyrae	80.7609	561	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	80.6168	554	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832745.1	s__Polaribacter sp009832745	80.1133	505	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831685.1	s__Polaribacter sp002831685	79.5925	502	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000060345.1	s__Gramella forsetii	76.952	59	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900113135.1	s__Salegentibacter agarivorans	76.1762	67	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_016236915.1	s__Salegentibacter maritimus	75.9123	64	966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	98.25	98.21	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-17 03:17:59,331] [INFO] GTDB search result was written to OceanDNA-b9981/result_gtdb.tsv
[2023-03-17 03:17:59,331] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:17:59,333] [INFO] DFAST_QC result json was written to OceanDNA-b9981/dqc_result.json
[2023-03-17 03:17:59,333] [INFO] DFAST_QC completed!
[2023-03-17 03:17:59,333] [INFO] Total running time: 0h1m32s