[2023-03-17 11:00:13,049] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:00:13,049] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:00:13,049] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b41a7c9-3825-4fc3-b0f1-73c79582cf08/dqc_reference
[2023-03-17 11:00:14,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:00:14,171] [INFO] Task started: Prodigal
[2023-03-17 11:00:14,172] [INFO] Running command: cat /var/lib/cwl/stg3bb17812-30ff-4ea9-89fa-fc54fed1a51e/OceanDNA-b10117.fa | prodigal -d OceanDNA-b10117/cds.fna -a OceanDNA-b10117/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:00:26,173] [INFO] Task succeeded: Prodigal
[2023-03-17 11:00:26,173] [INFO] Task started: HMMsearch
[2023-03-17 11:00:26,173] [INFO] Running command: hmmsearch --tblout OceanDNA-b10117/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b41a7c9-3825-4fc3-b0f1-73c79582cf08/dqc_reference/reference_markers.hmm OceanDNA-b10117/protein.faa > /dev/null
[2023-03-17 11:00:26,372] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:00:26,373] [INFO] Found 6/6 markers.
[2023-03-17 11:00:26,387] [INFO] Query marker FASTA was written to OceanDNA-b10117/markers.fasta
[2023-03-17 11:00:26,388] [INFO] Task started: Blastn
[2023-03-17 11:00:26,388] [INFO] Running command: blastn -query OceanDNA-b10117/markers.fasta -db /var/lib/cwl/stg1b41a7c9-3825-4fc3-b0f1-73c79582cf08/dqc_reference/reference_markers.fasta -out OceanDNA-b10117/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:00:26,974] [INFO] Task succeeded: Blastn
[2023-03-17 11:00:26,975] [INFO] Selected 23 target genomes.
[2023-03-17 11:00:26,975] [INFO] Target genome list was writen to OceanDNA-b10117/target_genomes.txt
[2023-03-17 11:00:27,082] [INFO] Task started: fastANI
[2023-03-17 11:00:27,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bb17812-30ff-4ea9-89fa-fc54fed1a51e/OceanDNA-b10117.fa --refList OceanDNA-b10117/target_genomes.txt --output OceanDNA-b10117/fastani_result.tsv --threads 1
[2023-03-17 11:00:40,170] [INFO] Task succeeded: fastANI
[2023-03-17 11:00:40,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b41a7c9-3825-4fc3-b0f1-73c79582cf08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:00:40,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b41a7c9-3825-4fc3-b0f1-73c79582cf08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:00:40,183] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:00:40,183] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:00:40,183] [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 aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	77.5632	208	665	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	77.3787	229	665	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.3653	221	665	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	77.2675	233	665	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	77.2598	231	665	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.2559	251	665	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.184	213	665	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	77.1815	221	665	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.1739	220	665	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.1595	206	665	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.1362	212	665	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.1006	219	665	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.072	216	665	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	77.0572	233	665	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	77.0422	235	665	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.0349	218	665	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.0224	218	665	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.0011	211	665	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	76.9856	220	665	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.9582	207	665	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	76.7052	154	665	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	76.6809	162	665	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	76.1305	122	665	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:00:40,186] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10117/tc_result.tsv
[2023-03-17 11:00:40,190] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:00:40,190] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:00:40,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b41a7c9-3825-4fc3-b0f1-73c79582cf08/dqc_reference/checkm_data
[2023-03-17 11:00:40,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:00:40,194] [INFO] Task started: CheckM
[2023-03-17 11:00:40,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10117/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10117/checkm_input OceanDNA-b10117/checkm_result
[2023-03-17 11:01:13,589] [INFO] Task succeeded: CheckM
[2023-03-17 11:01:13,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:01:13,594] [INFO] ===== Completeness check finished =====
[2023-03-17 11:01:13,595] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:01:13,595] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10117/markers.fasta)
[2023-03-17 11:01:13,596] [INFO] Task started: Blastn
[2023-03-17 11:01:13,596] [INFO] Running command: blastn -query OceanDNA-b10117/markers.fasta -db /var/lib/cwl/stg1b41a7c9-3825-4fc3-b0f1-73c79582cf08/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10117/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:01:14,437] [INFO] Task succeeded: Blastn
[2023-03-17 11:01:14,442] [INFO] Selected 14 target genomes.
[2023-03-17 11:01:14,443] [INFO] Target genome list was writen to OceanDNA-b10117/target_genomes_gtdb.txt
[2023-03-17 11:01:14,494] [INFO] Task started: fastANI
[2023-03-17 11:01:14,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bb17812-30ff-4ea9-89fa-fc54fed1a51e/OceanDNA-b10117.fa --refList OceanDNA-b10117/target_genomes_gtdb.txt --output OceanDNA-b10117/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:01:22,480] [INFO] Task succeeded: fastANI
[2023-03-17 11:01:22,488] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:01:22,489] [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_000383355.1	s__SCGC-AAA160-P02 sp000383355	84.6034	508	665	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	-
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	80.0871	425	665	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_905479435.1	s__SCGC-AAA160-P02 sp905479435	79.9869	305	665	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_018608485.1	s__SCGC-AAA160-P02 sp018608485	79.8694	334	665	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_016763215.1	s__SCGC-AAA160-P02 sp016763215	77.6472	159	665	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_002163675.1	s__Polaribacter sp002163675	77.5451	223	665	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	77.5338	202	665	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	77.5033	260	665	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	77.493	250	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	77.2674	250	665	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	77.2183	218	665	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	77.1713	214	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	77.0714	216	665	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	77.0102	238	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:01:22,493] [INFO] GTDB search result was written to OceanDNA-b10117/result_gtdb.tsv
[2023-03-17 11:01:22,499] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:01:22,505] [INFO] DFAST_QC result json was written to OceanDNA-b10117/dqc_result.json
[2023-03-17 11:01:22,505] [INFO] DFAST_QC completed!
[2023-03-17 11:01:22,505] [INFO] Total running time: 0h1m9s