[2023-03-19 03:28:07,259] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:28:07,259] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:28:07,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e275d63-5e14-4c89-9982-e8327585e7bb/dqc_reference
[2023-03-19 03:28:08,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:28:08,378] [INFO] Task started: Prodigal
[2023-03-19 03:28:08,378] [INFO] Running command: cat /var/lib/cwl/stgfb2972d4-b2c2-4d95-9c54-2819c95df0b2/OceanDNA-b9844.fa | prodigal -d OceanDNA-b9844/cds.fna -a OceanDNA-b9844/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:28:21,436] [INFO] Task succeeded: Prodigal
[2023-03-19 03:28:21,436] [INFO] Task started: HMMsearch
[2023-03-19 03:28:21,436] [INFO] Running command: hmmsearch --tblout OceanDNA-b9844/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e275d63-5e14-4c89-9982-e8327585e7bb/dqc_reference/reference_markers.hmm OceanDNA-b9844/protein.faa > /dev/null
[2023-03-19 03:28:21,631] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:28:21,632] [INFO] Found 6/6 markers.
[2023-03-19 03:28:21,645] [INFO] Query marker FASTA was written to OceanDNA-b9844/markers.fasta
[2023-03-19 03:28:21,645] [INFO] Task started: Blastn
[2023-03-19 03:28:21,645] [INFO] Running command: blastn -query OceanDNA-b9844/markers.fasta -db /var/lib/cwl/stg7e275d63-5e14-4c89-9982-e8327585e7bb/dqc_reference/reference_markers.fasta -out OceanDNA-b9844/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:28:22,228] [INFO] Task succeeded: Blastn
[2023-03-19 03:28:22,228] [INFO] Selected 19 target genomes.
[2023-03-19 03:28:22,229] [INFO] Target genome list was writen to OceanDNA-b9844/target_genomes.txt
[2023-03-19 03:28:22,239] [INFO] Task started: fastANI
[2023-03-19 03:28:22,239] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb2972d4-b2c2-4d95-9c54-2819c95df0b2/OceanDNA-b9844.fa --refList OceanDNA-b9844/target_genomes.txt --output OceanDNA-b9844/fastani_result.tsv --threads 1
[2023-03-19 03:28:33,421] [INFO] Task succeeded: fastANI
[2023-03-19 03:28:33,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e275d63-5e14-4c89-9982-e8327585e7bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:28:33,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e275d63-5e14-4c89-9982-e8327585e7bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:28:33,433] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:28:33,433] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:28:33,433] [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	78.6862	310	623	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	78.5279	293	623	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.5236	300	623	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	78.4676	250	623	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.4484	254	623	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	78.3627	254	623	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.1968	269	623	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.1486	278	623	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.1154	276	623	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	78.1138	247	623	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	78.0591	297	623	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	78.0554	259	623	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	78.0444	247	623	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	77.9332	262	623	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	77.8923	253	623	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.8461	206	623	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.7822	238	623	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	77.5267	175	623	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	76.4424	80	623	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:28:33,433] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9844/tc_result.tsv
[2023-03-19 03:28:33,433] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:28:33,433] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:28:33,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e275d63-5e14-4c89-9982-e8327585e7bb/dqc_reference/checkm_data
[2023-03-19 03:28:33,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:28:33,437] [INFO] Task started: CheckM
[2023-03-19 03:28:33,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9844/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9844/checkm_input OceanDNA-b9844/checkm_result
[2023-03-19 03:29:09,497] [INFO] Task succeeded: CheckM
[2023-03-19 03:29:09,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:29:09,499] [INFO] ===== Completeness check finished =====
[2023-03-19 03:29:09,500] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:29:09,500] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9844/markers.fasta)
[2023-03-19 03:29:09,500] [INFO] Task started: Blastn
[2023-03-19 03:29:09,500] [INFO] Running command: blastn -query OceanDNA-b9844/markers.fasta -db /var/lib/cwl/stg7e275d63-5e14-4c89-9982-e8327585e7bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9844/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:29:10,473] [INFO] Task succeeded: Blastn
[2023-03-19 03:29:10,473] [INFO] Selected 18 target genomes.
[2023-03-19 03:29:10,473] [INFO] Target genome list was writen to OceanDNA-b9844/target_genomes_gtdb.txt
[2023-03-19 03:29:10,611] [INFO] Task started: fastANI
[2023-03-19 03:29:10,611] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb2972d4-b2c2-4d95-9c54-2819c95df0b2/OceanDNA-b9844.fa --refList OceanDNA-b9844/target_genomes_gtdb.txt --output OceanDNA-b9844/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:29:21,617] [INFO] Task succeeded: fastANI
[2023-03-19 03:29:21,627] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:29:21,627] [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	87.8847	556	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.23	98.14	0.90	0.83	5	-
GCF_014352875.1	s__Polaribacter sp014352875	78.6739	311	623	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	78.5313	238	623	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	78.5279	293	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002163835.1	s__Polaribacter sp002163835	78.5123	288	623	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	78.4676	250	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831685.1	s__Polaribacter sp002831685	78.4607	272	623	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	78.3853	290	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	78.2636	273	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_002163675.1	s__Polaribacter sp002163675	78.2496	267	623	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	78.1968	269	623	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	78.1929	261	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498485.1	s__Polaribacter sp017498485	78.1486	278	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885675.1	s__Polaribacter aestuariivivens	78.0476	298	623	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	78.0049	218	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	77.9933	234	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	77.6601	239	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	77.5267	175	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-19 03:29:21,627] [INFO] GTDB search result was written to OceanDNA-b9844/result_gtdb.tsv
[2023-03-19 03:29:21,628] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:29:21,630] [INFO] DFAST_QC result json was written to OceanDNA-b9844/dqc_result.json
[2023-03-19 03:29:21,630] [INFO] DFAST_QC completed!
[2023-03-19 03:29:21,630] [INFO] Total running time: 0h1m14s