[2023-03-15 09:48:18,535] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:18,536] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:18,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ae20af0-4261-46e0-b20d-9c4eb095e8ae/dqc_reference
[2023-03-15 09:48:19,626] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:19,626] [INFO] Task started: Prodigal
[2023-03-15 09:48:19,627] [INFO] Running command: cat /var/lib/cwl/stg6e910076-29c6-4fba-a688-6fd2b6555fc1/OceanDNA-b10199.fa | prodigal -d OceanDNA-b10199/cds.fna -a OceanDNA-b10199/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:29,482] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:29,482] [INFO] Task started: HMMsearch
[2023-03-15 09:48:29,482] [INFO] Running command: hmmsearch --tblout OceanDNA-b10199/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ae20af0-4261-46e0-b20d-9c4eb095e8ae/dqc_reference/reference_markers.hmm OceanDNA-b10199/protein.faa > /dev/null
[2023-03-15 09:48:29,706] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:29,707] [INFO] Found 6/6 markers.
[2023-03-15 09:48:29,721] [INFO] Query marker FASTA was written to OceanDNA-b10199/markers.fasta
[2023-03-15 09:48:29,722] [INFO] Task started: Blastn
[2023-03-15 09:48:29,722] [INFO] Running command: blastn -query OceanDNA-b10199/markers.fasta -db /var/lib/cwl/stg0ae20af0-4261-46e0-b20d-9c4eb095e8ae/dqc_reference/reference_markers.fasta -out OceanDNA-b10199/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:30,299] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:30,300] [INFO] Selected 22 target genomes.
[2023-03-15 09:48:30,300] [INFO] Target genome list was writen to OceanDNA-b10199/target_genomes.txt
[2023-03-15 09:48:30,309] [INFO] Task started: fastANI
[2023-03-15 09:48:30,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e910076-29c6-4fba-a688-6fd2b6555fc1/OceanDNA-b10199.fa --refList OceanDNA-b10199/target_genomes.txt --output OceanDNA-b10199/fastani_result.tsv --threads 1
[2023-03-15 09:48:42,339] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:42,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ae20af0-4261-46e0-b20d-9c4eb095e8ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:42,339] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ae20af0-4261-46e0-b20d-9c4eb095e8ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:42,351] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:42,352] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:48:42,352] [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 pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.7757	181	503	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.7481	152	503	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	77.733	162	503	95	below_threshold
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	77.6969	164	503	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.6901	168	503	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	77.6853	176	503	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	77.6738	162	503	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	77.6534	164	503	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.6475	161	503	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.6454	181	503	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.5884	152	503	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	77.5776	110	503	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.556	164	503	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.5145	158	503	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	77.5105	170	503	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.4604	173	503	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	77.4445	175	503	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.3464	177	503	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.2563	163	503	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.2266	177	503	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	77.03	140	503	95	below_threshold
Tenacibaculum adriaticum	strain=DSM 18961	GCA_008124875.1	413713	413713	type	True	76.908	113	503	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:48:42,352] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10199/tc_result.tsv
[2023-03-15 09:48:42,352] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:42,352] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:42,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ae20af0-4261-46e0-b20d-9c4eb095e8ae/dqc_reference/checkm_data
[2023-03-15 09:48:42,353] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:42,356] [INFO] Task started: CheckM
[2023-03-15 09:48:42,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10199/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10199/checkm_input OceanDNA-b10199/checkm_result
[2023-03-15 09:49:11,603] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:11,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:11,605] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:11,605] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:11,605] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10199/markers.fasta)
[2023-03-15 09:49:11,605] [INFO] Task started: Blastn
[2023-03-15 09:49:11,605] [INFO] Running command: blastn -query OceanDNA-b10199/markers.fasta -db /var/lib/cwl/stg0ae20af0-4261-46e0-b20d-9c4eb095e8ae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10199/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:12,417] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:12,418] [INFO] Selected 15 target genomes.
[2023-03-15 09:49:12,418] [INFO] Target genome list was writen to OceanDNA-b10199/target_genomes_gtdb.txt
[2023-03-15 09:49:12,677] [INFO] Task started: fastANI
[2023-03-15 09:49:12,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e910076-29c6-4fba-a688-6fd2b6555fc1/OceanDNA-b10199.fa --refList OceanDNA-b10199/target_genomes_gtdb.txt --output OceanDNA-b10199/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:20,785] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:20,795] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:49:20,795] [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_015665265.1	s__SCGC-AAA160-P02 sp015665265	96.4591	447	503	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	conclusive
GCA_018608485.1	s__SCGC-AAA160-P02 sp018608485	92.4735	353	503	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_905479435.1	s__SCGC-AAA160-P02 sp905479435	83.7227	291	503	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_000383355.1	s__SCGC-AAA160-P02 sp000383355	82.2057	386	503	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_002163675.1	s__Polaribacter sp002163675	77.8237	167	503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	77.6796	136	503	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	77.6722	194	503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954685.1	s__Polaribacter porphyrae	77.6676	177	503	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	77.564	189	503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	77.5145	158	503	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	77.4677	89	503	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	-
GCF_900105145.1	s__Polaribacter sp900105145	77.4369	176	503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	77.3838	199	503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105985.1	s__Tenacibaculum sp900105985	77.0309	134	503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCF_002836595.1	s__Tenacibaculum sp002836595	76.8345	150	503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:20,795] [INFO] GTDB search result was written to OceanDNA-b10199/result_gtdb.tsv
[2023-03-15 09:49:20,795] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:20,797] [INFO] DFAST_QC result json was written to OceanDNA-b10199/dqc_result.json
[2023-03-15 09:49:20,797] [INFO] DFAST_QC completed!
[2023-03-15 09:49:20,797] [INFO] Total running time: 0h1m2s