[2023-03-16 17:15:23,150] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:15:23,150] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:15:23,150] [INFO] DQC Reference Directory: /var/lib/cwl/stg063c2298-41d5-49ea-94fb-5ebfa69b3b3c/dqc_reference
[2023-03-16 17:15:24,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:15:24,275] [INFO] Task started: Prodigal
[2023-03-16 17:15:24,275] [INFO] Running command: cat /var/lib/cwl/stg5636f8d0-be26-41d6-ab98-e50de01322c1/OceanDNA-b10144.fa | prodigal -d OceanDNA-b10144/cds.fna -a OceanDNA-b10144/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:15:36,857] [INFO] Task succeeded: Prodigal
[2023-03-16 17:15:36,858] [INFO] Task started: HMMsearch
[2023-03-16 17:15:36,858] [INFO] Running command: hmmsearch --tblout OceanDNA-b10144/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg063c2298-41d5-49ea-94fb-5ebfa69b3b3c/dqc_reference/reference_markers.hmm OceanDNA-b10144/protein.faa > /dev/null
[2023-03-16 17:15:37,049] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:15:37,050] [INFO] Found 6/6 markers.
[2023-03-16 17:15:37,064] [INFO] Query marker FASTA was written to OceanDNA-b10144/markers.fasta
[2023-03-16 17:15:37,065] [INFO] Task started: Blastn
[2023-03-16 17:15:37,065] [INFO] Running command: blastn -query OceanDNA-b10144/markers.fasta -db /var/lib/cwl/stg063c2298-41d5-49ea-94fb-5ebfa69b3b3c/dqc_reference/reference_markers.fasta -out OceanDNA-b10144/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:15:37,647] [INFO] Task succeeded: Blastn
[2023-03-16 17:15:37,648] [INFO] Selected 24 target genomes.
[2023-03-16 17:15:37,648] [INFO] Target genome list was writen to OceanDNA-b10144/target_genomes.txt
[2023-03-16 17:15:37,695] [INFO] Task started: fastANI
[2023-03-16 17:15:37,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg5636f8d0-be26-41d6-ab98-e50de01322c1/OceanDNA-b10144.fa --refList OceanDNA-b10144/target_genomes.txt --output OceanDNA-b10144/fastani_result.tsv --threads 1
[2023-03-16 17:15:51,650] [INFO] Task succeeded: fastANI
[2023-03-16 17:15:51,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg063c2298-41d5-49ea-94fb-5ebfa69b3b3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:15:51,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg063c2298-41d5-49ea-94fb-5ebfa69b3b3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:15:51,664] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:15:51,664] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:15:51,664] [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 aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.1745	181	673	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.11	193	673	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	76.9555	171	673	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.9537	198	673	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	76.9344	196	673	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.8209	171	673	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.8194	176	673	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.8054	172	673	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	76.7949	179	673	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	76.7612	167	673	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	76.705	205	673	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	76.6946	201	673	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.6681	164	673	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	76.5972	118	673	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.5908	169	673	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	76.5826	177	673	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	76.5738	165	673	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	76.5724	129	673	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.5717	158	673	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.5667	170	673	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	76.5534	176	673	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.4674	123	673	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.4433	160	673	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	76.384	114	673	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:15:51,664] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10144/tc_result.tsv
[2023-03-16 17:15:51,664] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:15:51,664] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:15:51,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg063c2298-41d5-49ea-94fb-5ebfa69b3b3c/dqc_reference/checkm_data
[2023-03-16 17:15:51,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:15:52,073] [INFO] Task started: CheckM
[2023-03-16 17:15:52,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10144/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10144/checkm_input OceanDNA-b10144/checkm_result
[2023-03-16 17:16:39,013] [INFO] Task succeeded: CheckM
[2023-03-16 17:16:39,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:16:39,016] [INFO] ===== Completeness check finished =====
[2023-03-16 17:16:39,016] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:16:39,016] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10144/markers.fasta)
[2023-03-16 17:16:39,017] [INFO] Task started: Blastn
[2023-03-16 17:16:39,017] [INFO] Running command: blastn -query OceanDNA-b10144/markers.fasta -db /var/lib/cwl/stg063c2298-41d5-49ea-94fb-5ebfa69b3b3c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10144/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:16:39,855] [INFO] Task succeeded: Blastn
[2023-03-16 17:16:39,856] [INFO] Selected 15 target genomes.
[2023-03-16 17:16:39,856] [INFO] Target genome list was writen to OceanDNA-b10144/target_genomes_gtdb.txt
[2023-03-16 17:16:39,868] [INFO] Task started: fastANI
[2023-03-16 17:16:39,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg5636f8d0-be26-41d6-ab98-e50de01322c1/OceanDNA-b10144.fa --refList OceanDNA-b10144/target_genomes_gtdb.txt --output OceanDNA-b10144/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:16:47,386] [INFO] Task succeeded: fastANI
[2023-03-16 17:16:47,395] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:16:47,395] [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_905479435.1	s__SCGC-AAA160-P02 sp905479435	85.2626	404	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	83.0051	477	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.43	96.43	0.88	0.88	2	-
GCA_018608485.1	s__SCGC-AAA160-P02 sp018608485	82.0144	386	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	99.40	99.40	0.78	0.78	2	-
GCA_000383355.1	s__SCGC-AAA160-P02 sp000383355	80.8306	444	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.64	95.28	0.86	0.84	6	-
GCF_000766795.1	s__Polaribacter sp000766795	77.4955	203	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373105.1	s__Polaribacter sp013373105	77.1428	160	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827455.1	s__VISM01 sp007827455	77.0569	186	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861005.1	s__Polaribacter vadi_A	77.024	192	673	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	76.9835	214	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	76.9802	205	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152945.2	s__Polaribacter sp000152945	76.9498	176	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763215.1	s__SCGC-AAA160-P02 sp016763215	76.8714	111	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018663625.1	s__Polaribacter sp018663625	76.7619	131	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.23	98.14	0.90	0.83	5	-
GCA_019263805.1	s__Polaribacter sp011379025	76.6706	160	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_900239345.1	s__Tenacibaculum dicentrarchi	76.4164	127	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.61	97.94	0.93	0.91	10	-
--------------------------------------------------------------------------------
[2023-03-16 17:16:47,395] [INFO] GTDB search result was written to OceanDNA-b10144/result_gtdb.tsv
[2023-03-16 17:16:47,396] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:16:47,398] [INFO] DFAST_QC result json was written to OceanDNA-b10144/dqc_result.json
[2023-03-16 17:16:47,398] [INFO] DFAST_QC completed!
[2023-03-16 17:16:47,398] [INFO] Total running time: 0h1m24s