[2023-03-15 10:56:32,935] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:56:32,935] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:56:32,935] [INFO] DQC Reference Directory: /var/lib/cwl/stge56034b1-2134-4da4-af4a-1a1385f816eb/dqc_reference
[2023-03-15 10:56:34,050] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:56:34,050] [INFO] Task started: Prodigal
[2023-03-15 10:56:34,051] [INFO] Running command: cat /var/lib/cwl/stg10320e8c-5535-4e81-bd97-7b3b94cc90df/OceanDNA-b9866.fa | prodigal -d OceanDNA-b9866/cds.fna -a OceanDNA-b9866/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:56:47,578] [INFO] Task succeeded: Prodigal
[2023-03-15 10:56:47,578] [INFO] Task started: HMMsearch
[2023-03-15 10:56:47,578] [INFO] Running command: hmmsearch --tblout OceanDNA-b9866/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge56034b1-2134-4da4-af4a-1a1385f816eb/dqc_reference/reference_markers.hmm OceanDNA-b9866/protein.faa > /dev/null
[2023-03-15 10:56:47,755] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:56:47,755] [INFO] Found 6/6 markers.
[2023-03-15 10:56:47,768] [INFO] Query marker FASTA was written to OceanDNA-b9866/markers.fasta
[2023-03-15 10:56:47,769] [INFO] Task started: Blastn
[2023-03-15 10:56:47,769] [INFO] Running command: blastn -query OceanDNA-b9866/markers.fasta -db /var/lib/cwl/stge56034b1-2134-4da4-af4a-1a1385f816eb/dqc_reference/reference_markers.fasta -out OceanDNA-b9866/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:56:48,351] [INFO] Task succeeded: Blastn
[2023-03-15 10:56:48,352] [INFO] Selected 12 target genomes.
[2023-03-15 10:56:48,352] [INFO] Target genome list was writen to OceanDNA-b9866/target_genomes.txt
[2023-03-15 10:56:48,358] [INFO] Task started: fastANI
[2023-03-15 10:56:48,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg10320e8c-5535-4e81-bd97-7b3b94cc90df/OceanDNA-b9866.fa --refList OceanDNA-b9866/target_genomes.txt --output OceanDNA-b9866/fastani_result.tsv --threads 1
[2023-03-15 10:56:55,916] [INFO] Task succeeded: fastANI
[2023-03-15 10:56:55,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge56034b1-2134-4da4-af4a-1a1385f816eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:56:55,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge56034b1-2134-4da4-af4a-1a1385f816eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:56:55,925] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:56:55,925] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:56:55,925] [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	78.9128	372	663	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.901	345	663	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	78.8846	344	663	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	78.8158	292	663	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.7739	287	663	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	78.6969	305	663	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.5765	325	663	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.5355	333	663	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	78.4595	346	663	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.3999	288	663	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.3459	265	663	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.2821	328	663	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:56:55,925] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9866/tc_result.tsv
[2023-03-15 10:56:55,925] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:56:55,925] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:56:55,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge56034b1-2134-4da4-af4a-1a1385f816eb/dqc_reference/checkm_data
[2023-03-15 10:56:55,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:56:55,929] [INFO] Task started: CheckM
[2023-03-15 10:56:55,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9866/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9866/checkm_input OceanDNA-b9866/checkm_result
[2023-03-15 10:57:33,153] [INFO] Task succeeded: CheckM
[2023-03-15 10:57:33,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:57:33,155] [INFO] ===== Completeness check finished =====
[2023-03-15 10:57:33,155] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:57:33,155] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9866/markers.fasta)
[2023-03-15 10:57:33,155] [INFO] Task started: Blastn
[2023-03-15 10:57:33,155] [INFO] Running command: blastn -query OceanDNA-b9866/markers.fasta -db /var/lib/cwl/stge56034b1-2134-4da4-af4a-1a1385f816eb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9866/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:57:34,178] [INFO] Task succeeded: Blastn
[2023-03-15 10:57:34,179] [INFO] Selected 17 target genomes.
[2023-03-15 10:57:34,179] [INFO] Target genome list was writen to OceanDNA-b9866/target_genomes_gtdb.txt
[2023-03-15 10:57:34,192] [INFO] Task started: fastANI
[2023-03-15 10:57:34,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg10320e8c-5535-4e81-bd97-7b3b94cc90df/OceanDNA-b9866.fa --refList OceanDNA-b9866/target_genomes_gtdb.txt --output OceanDNA-b9866/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:57:44,655] [INFO] Task succeeded: fastANI
[2023-03-15 10:57:44,665] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:57:44,665] [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_018663625.1	s__Polaribacter sp018663625	99.921	621	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.23	98.14	0.90	0.83	5	conclusive
GCF_002163835.1	s__Polaribacter sp002163835	78.919	364	663	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	78.9073	371	663	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	78.8784	345	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002831685.1	s__Polaribacter sp002831685	78.8587	340	663	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	78.8452	328	663	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	78.8158	292	663	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	78.8103	321	663	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	78.6969	305	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_009796785.1	s__Polaribacter sp009796785	78.6824	327	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	78.662	336	663	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	78.6575	313	663	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	78.5643	326	663	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	78.5286	333	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005425.1	s__Polaribacter sp002005425	78.4918	297	663	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_017498485.1	s__Polaribacter sp017498485	78.283	328	663	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	78.2042	254	663	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 10:57:44,665] [INFO] GTDB search result was written to OceanDNA-b9866/result_gtdb.tsv
[2023-03-15 10:57:44,665] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:57:44,667] [INFO] DFAST_QC result json was written to OceanDNA-b9866/dqc_result.json
[2023-03-15 10:57:44,667] [INFO] DFAST_QC completed!
[2023-03-15 10:57:44,667] [INFO] Total running time: 0h1m12s