[2023-03-15 17:24:01,374] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:24:01,374] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:24:01,375] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb9f4729-2e86-4215-a394-c959352ac854/dqc_reference
[2023-03-15 17:24:02,554] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:24:02,554] [INFO] Task started: Prodigal
[2023-03-15 17:24:02,555] [INFO] Running command: cat /var/lib/cwl/stg60261fca-4b59-4e42-a503-edc8cccc4af5/OceanDNA-b9903.fa | prodigal -d OceanDNA-b9903/cds.fna -a OceanDNA-b9903/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:24:13,564] [INFO] Task succeeded: Prodigal
[2023-03-15 17:24:13,564] [INFO] Task started: HMMsearch
[2023-03-15 17:24:13,564] [INFO] Running command: hmmsearch --tblout OceanDNA-b9903/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb9f4729-2e86-4215-a394-c959352ac854/dqc_reference/reference_markers.hmm OceanDNA-b9903/protein.faa > /dev/null
[2023-03-15 17:24:13,869] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:24:13,870] [INFO] Found 6/6 markers.
[2023-03-15 17:24:13,885] [INFO] Query marker FASTA was written to OceanDNA-b9903/markers.fasta
[2023-03-15 17:24:13,886] [INFO] Task started: Blastn
[2023-03-15 17:24:13,886] [INFO] Running command: blastn -query OceanDNA-b9903/markers.fasta -db /var/lib/cwl/stgcb9f4729-2e86-4215-a394-c959352ac854/dqc_reference/reference_markers.fasta -out OceanDNA-b9903/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:14,532] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:14,533] [INFO] Selected 21 target genomes.
[2023-03-15 17:24:14,533] [INFO] Target genome list was writen to OceanDNA-b9903/target_genomes.txt
[2023-03-15 17:24:14,544] [INFO] Task started: fastANI
[2023-03-15 17:24:14,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg60261fca-4b59-4e42-a503-edc8cccc4af5/OceanDNA-b9903.fa --refList OceanDNA-b9903/target_genomes.txt --output OceanDNA-b9903/fastani_result.tsv --threads 1
[2023-03-15 17:24:27,271] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:27,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb9f4729-2e86-4215-a394-c959352ac854/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:24:27,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb9f4729-2e86-4215-a394-c959352ac854/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:24:27,284] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:24:27,284] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:24:27,284] [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	79.0899	291	530	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	78.9649	299	530	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	78.9204	294	530	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.9065	316	530	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.9027	300	530	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	78.5047	286	530	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.4761	240	530	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	78.4637	268	530	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	78.4552	273	530	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	78.4089	266	530	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	78.4081	269	530	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.406	271	530	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	78.3175	275	530	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	78.2995	280	530	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.2922	282	530	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	78.2365	242	530	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	78.2023	263	530	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.0049	243	530	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	77.8315	249	530	95	below_threshold
Polaribacter tangerinus	strain=WS2-14	GCA_002201235.1	1920034	1920034	type	True	77.723	181	530	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.5446	204	530	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:24:27,284] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9903/tc_result.tsv
[2023-03-15 17:24:27,284] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:24:27,284] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:24:27,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb9f4729-2e86-4215-a394-c959352ac854/dqc_reference/checkm_data
[2023-03-15 17:24:27,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:24:27,289] [INFO] Task started: CheckM
[2023-03-15 17:24:27,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9903/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9903/checkm_input OceanDNA-b9903/checkm_result
[2023-03-15 17:24:58,951] [INFO] Task succeeded: CheckM
[2023-03-15 17:24:58,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:24:59,212] [INFO] ===== Completeness check finished =====
[2023-03-15 17:24:59,212] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:24:59,212] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9903/markers.fasta)
[2023-03-15 17:24:59,213] [INFO] Task started: Blastn
[2023-03-15 17:24:59,214] [INFO] Running command: blastn -query OceanDNA-b9903/markers.fasta -db /var/lib/cwl/stgcb9f4729-2e86-4215-a394-c959352ac854/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9903/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:25:00,080] [INFO] Task succeeded: Blastn
[2023-03-15 17:25:00,081] [INFO] Selected 19 target genomes.
[2023-03-15 17:25:00,081] [INFO] Target genome list was writen to OceanDNA-b9903/target_genomes_gtdb.txt
[2023-03-15 17:25:00,103] [INFO] Task started: fastANI
[2023-03-15 17:25:00,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg60261fca-4b59-4e42-a503-edc8cccc4af5/OceanDNA-b9903.fa --refList OceanDNA-b9903/target_genomes_gtdb.txt --output OceanDNA-b9903/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:25:11,108] [INFO] Task succeeded: fastANI
[2023-03-15 17:25:11,119] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:25:11,119] [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_018608545.1	s__Polaribacter sp018608545	84.8402	451	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.39	97.39	0.93	0.93	2	-
GCF_000766795.1	s__Polaribacter sp000766795	79.7228	343	530	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	79.0899	291	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796785.1	s__Polaribacter sp009796785	79.0422	314	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	78.9864	297	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814075.1	s__Polaribacter sejongensis	78.9258	294	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_002954605.1	s__Polaribacter butkevichii	78.9076	316	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	78.8901	313	530	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	78.6986	311	530	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	78.6452	232	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	78.5047	286	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997075.1	s__Polaribacter sp007997075	78.4987	271	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569185.1	s__Polaribacter sp017569185	78.4761	240	530	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	78.4359	269	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005885675.1	s__Polaribacter aestuariivivens	78.3319	274	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	78.3129	279	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002943715.1	s__Polaribacter filamentus	78.2022	263	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335085.1	s__Polaribacter sp003335085	78.0602	256	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002201235.1	s__Polaribacter tangerinus	77.7057	182	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:25:11,119] [INFO] GTDB search result was written to OceanDNA-b9903/result_gtdb.tsv
[2023-03-15 17:25:11,119] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:25:11,122] [INFO] DFAST_QC result json was written to OceanDNA-b9903/dqc_result.json
[2023-03-15 17:25:11,122] [INFO] DFAST_QC completed!
[2023-03-15 17:25:11,122] [INFO] Total running time: 0h1m10s