[2023-03-18 21:47:29,601] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:47:29,601] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:47:29,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg05518c59-a958-4e25-8c6d-7b0dc7d9facf/dqc_reference
[2023-03-18 21:47:30,693] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:47:30,694] [INFO] Task started: Prodigal
[2023-03-18 21:47:30,694] [INFO] Running command: cat /var/lib/cwl/stg18650cca-14da-4a23-b48f-39b91aaed451/OceanDNA-b7442.fa | prodigal -d OceanDNA-b7442/cds.fna -a OceanDNA-b7442/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:47:45,357] [INFO] Task succeeded: Prodigal
[2023-03-18 21:47:45,357] [INFO] Task started: HMMsearch
[2023-03-18 21:47:45,357] [INFO] Running command: hmmsearch --tblout OceanDNA-b7442/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05518c59-a958-4e25-8c6d-7b0dc7d9facf/dqc_reference/reference_markers.hmm OceanDNA-b7442/protein.faa > /dev/null
[2023-03-18 21:47:45,550] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:47:45,550] [INFO] Found 6/6 markers.
[2023-03-18 21:47:45,567] [INFO] Query marker FASTA was written to OceanDNA-b7442/markers.fasta
[2023-03-18 21:47:45,568] [INFO] Task started: Blastn
[2023-03-18 21:47:45,568] [INFO] Running command: blastn -query OceanDNA-b7442/markers.fasta -db /var/lib/cwl/stg05518c59-a958-4e25-8c6d-7b0dc7d9facf/dqc_reference/reference_markers.fasta -out OceanDNA-b7442/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:47:46,171] [INFO] Task succeeded: Blastn
[2023-03-18 21:47:46,173] [INFO] Selected 38 target genomes.
[2023-03-18 21:47:46,173] [INFO] Target genome list was writen to OceanDNA-b7442/target_genomes.txt
[2023-03-18 21:47:46,195] [INFO] Task started: fastANI
[2023-03-18 21:47:46,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg18650cca-14da-4a23-b48f-39b91aaed451/OceanDNA-b7442.fa --refList OceanDNA-b7442/target_genomes.txt --output OceanDNA-b7442/fastani_result.tsv --threads 1
[2023-03-18 21:48:08,864] [INFO] Task succeeded: fastANI
[2023-03-18 21:48:08,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05518c59-a958-4e25-8c6d-7b0dc7d9facf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:48:08,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05518c59-a958-4e25-8c6d-7b0dc7d9facf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:48:08,880] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:48:08,880] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:48:08,880] [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 thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.2989	74	599	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	76.1978	57	599	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.1546	65	599	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	76.1325	79	599	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.13	65	599	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.1067	73	599	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	76.0908	73	599	95	below_threshold
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	76.0863	62	599	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.0811	73	599	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.0754	74	599	95	below_threshold
Winogradskyella epiphytica	strain=CECT 7945	GCA_003217215.1	262005	262005	type	True	76.0578	51	599	95	below_threshold
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	76.0528	63	599	95	below_threshold
Formosa haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	76.0505	74	599	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	76.0307	52	599	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	75.9929	71	599	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	75.9688	57	599	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	75.9674	78	599	95	below_threshold
Aurantibacter aestuarii	strain=KCTC 32269	GCA_003008425.1	1266046	1266046	type	True	75.9613	58	599	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	75.9363	78	599	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	75.9305	69	599	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	75.9091	73	599	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	75.9029	82	599	95	below_threshold
Gelidibacter salicanalis	strain=IC162	GCA_007997285.1	291193	291193	type	True	75.8969	61	599	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	75.8865	83	599	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	75.8837	64	599	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	75.8702	73	599	95	below_threshold
Bizionia paragorgiae	strain=DSM 23842	GCA_900107625.1	283786	283786	type	True	75.7595	70	599	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	75.6614	71	599	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	75.6488	72	599	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	75.3206	53	599	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:48:08,882] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7442/tc_result.tsv
[2023-03-18 21:48:08,883] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:48:08,883] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:48:08,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05518c59-a958-4e25-8c6d-7b0dc7d9facf/dqc_reference/checkm_data
[2023-03-18 21:48:08,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:48:08,950] [INFO] Task started: CheckM
[2023-03-18 21:48:08,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7442/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7442/checkm_input OceanDNA-b7442/checkm_result
[2023-03-18 21:48:46,288] [INFO] Task succeeded: CheckM
[2023-03-18 21:48:46,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.40%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 21:48:46,405] [INFO] ===== Completeness check finished =====
[2023-03-18 21:48:46,405] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:48:46,405] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7442/markers.fasta)
[2023-03-18 21:48:46,406] [INFO] Task started: Blastn
[2023-03-18 21:48:46,406] [INFO] Running command: blastn -query OceanDNA-b7442/markers.fasta -db /var/lib/cwl/stg05518c59-a958-4e25-8c6d-7b0dc7d9facf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7442/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:48:47,301] [INFO] Task succeeded: Blastn
[2023-03-18 21:48:47,374] [INFO] Selected 9 target genomes.
[2023-03-18 21:48:47,374] [INFO] Target genome list was writen to OceanDNA-b7442/target_genomes_gtdb.txt
[2023-03-18 21:48:47,383] [INFO] Task started: fastANI
[2023-03-18 21:48:47,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg18650cca-14da-4a23-b48f-39b91aaed451/OceanDNA-b7442.fa --refList OceanDNA-b7442/target_genomes_gtdb.txt --output OceanDNA-b7442/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:48:51,526] [INFO] Task succeeded: fastANI
[2023-03-18 21:48:51,532] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:48:51,532] [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_001735745.1	s__Hel1-33-131 sp001735745	99.6389	577	599	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	conclusive
GCA_018608765.1	s__Hel1-33-131 sp018608765	84.8642	448	599	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	84.3085	419	599	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	84.0524	376	599	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	81.9136	320	599	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	81.3778	392	599	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_905181825.1	s__Hel1-33-131 sp905181825	78.5621	216	599	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	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	78.3036	242	599	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	-
GCF_015355625.1	s__Tamlana_A sp015355625	75.9854	80	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:48:51,549] [INFO] GTDB search result was written to OceanDNA-b7442/result_gtdb.tsv
[2023-03-18 21:48:51,602] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:48:51,628] [INFO] DFAST_QC result json was written to OceanDNA-b7442/dqc_result.json
[2023-03-18 21:48:51,628] [INFO] DFAST_QC completed!
[2023-03-18 21:48:51,628] [INFO] Total running time: 0h1m22s