[2023-03-17 01:23:45,140] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:23:45,140] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:23:45,140] [INFO] DQC Reference Directory: /var/lib/cwl/stg70dff582-74e5-4f2b-9436-1410696ea3a6/dqc_reference
[2023-03-17 01:23:46,316] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:23:46,316] [INFO] Task started: Prodigal
[2023-03-17 01:23:46,317] [INFO] Running command: cat /var/lib/cwl/stg2165ae36-531f-47aa-a61a-a846568472f2/OceanDNA-b29397.fa | prodigal -d OceanDNA-b29397/cds.fna -a OceanDNA-b29397/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:24:05,486] [INFO] Task succeeded: Prodigal
[2023-03-17 01:24:05,487] [INFO] Task started: HMMsearch
[2023-03-17 01:24:05,487] [INFO] Running command: hmmsearch --tblout OceanDNA-b29397/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70dff582-74e5-4f2b-9436-1410696ea3a6/dqc_reference/reference_markers.hmm OceanDNA-b29397/protein.faa > /dev/null
[2023-03-17 01:24:05,677] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:24:05,677] [INFO] Found 6/6 markers.
[2023-03-17 01:24:05,697] [INFO] Query marker FASTA was written to OceanDNA-b29397/markers.fasta
[2023-03-17 01:24:05,698] [INFO] Task started: Blastn
[2023-03-17 01:24:05,698] [INFO] Running command: blastn -query OceanDNA-b29397/markers.fasta -db /var/lib/cwl/stg70dff582-74e5-4f2b-9436-1410696ea3a6/dqc_reference/reference_markers.fasta -out OceanDNA-b29397/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:24:06,375] [INFO] Task succeeded: Blastn
[2023-03-17 01:24:06,375] [INFO] Selected 18 target genomes.
[2023-03-17 01:24:06,376] [INFO] Target genome list was writen to OceanDNA-b29397/target_genomes.txt
[2023-03-17 01:24:06,387] [INFO] Task started: fastANI
[2023-03-17 01:24:06,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg2165ae36-531f-47aa-a61a-a846568472f2/OceanDNA-b29397.fa --refList OceanDNA-b29397/target_genomes.txt --output OceanDNA-b29397/fastani_result.tsv --threads 1
[2023-03-17 01:24:19,459] [INFO] Task succeeded: fastANI
[2023-03-17 01:24:19,459] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70dff582-74e5-4f2b-9436-1410696ea3a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:24:19,459] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70dff582-74e5-4f2b-9436-1410696ea3a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:24:19,470] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 01:24:19,470] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 01:24:19,470] [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
Jannaschia helgolandensis	strain=DSM 14858	GCA_900109285.1	188906	188906	type	True	97.9576	961	1000	95	conclusive
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	79.3531	544	1000	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	79.1655	493	1000	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	79.1272	497	1000	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	78.6563	520	1000	95	below_threshold
Jannaschia faecimaris	strain=DSM 100420	GCA_900107415.1	1244108	1244108	type	True	78.6131	491	1000	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.1563	455	1000	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	78.0247	401	1000	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.2648	239	1000	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	77.0033	222	1000	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.8555	197	1000	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.8288	201	1000	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.8055	203	1000	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.7658	203	1000	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	76.6886	220	1000	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	76.6666	211	1000	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.5761	201	1000	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	76.5649	162	1000	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:24:19,470] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29397/tc_result.tsv
[2023-03-17 01:24:19,470] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:24:19,470] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:24:19,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70dff582-74e5-4f2b-9436-1410696ea3a6/dqc_reference/checkm_data
[2023-03-17 01:24:19,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:24:19,475] [INFO] Task started: CheckM
[2023-03-17 01:24:19,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29397/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29397/checkm_input OceanDNA-b29397/checkm_result
[2023-03-17 01:25:08,167] [INFO] Task succeeded: CheckM
[2023-03-17 01:25:08,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:25:08,169] [INFO] ===== Completeness check finished =====
[2023-03-17 01:25:08,169] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:25:08,170] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29397/markers.fasta)
[2023-03-17 01:25:08,171] [INFO] Task started: Blastn
[2023-03-17 01:25:08,171] [INFO] Running command: blastn -query OceanDNA-b29397/markers.fasta -db /var/lib/cwl/stg70dff582-74e5-4f2b-9436-1410696ea3a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29397/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:25:09,272] [INFO] Task succeeded: Blastn
[2023-03-17 01:25:09,273] [INFO] Selected 15 target genomes.
[2023-03-17 01:25:09,273] [INFO] Target genome list was writen to OceanDNA-b29397/target_genomes_gtdb.txt
[2023-03-17 01:25:09,453] [INFO] Task started: fastANI
[2023-03-17 01:25:09,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg2165ae36-531f-47aa-a61a-a846568472f2/OceanDNA-b29397.fa --refList OceanDNA-b29397/target_genomes_gtdb.txt --output OceanDNA-b29397/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:25:20,678] [INFO] Task succeeded: fastANI
[2023-03-17 01:25:20,687] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 01:25:20,687] [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
GCF_900109285.1	s__Jannaschia helgolandensis	97.9576	961	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001403795.1	s__Jannaschia donghaensis	79.5178	562	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113875.1	s__Jannaschia pohangensis	79.3531	544	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403735.1	s__Jannaschia rubra	79.1084	499	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013404595.1	s__Jannaschia marina	78.6643	519	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107415.1	s__Jannaschia faecimaris	78.605	492	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	78.1646	454	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116765.1	s__Jannaschia seohaensis	78.0337	400	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001408515.1	s__Jannaschia seosinensis	77.9688	344	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	77.044	234	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	76.8763	177	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_001679925.1	s__Leisingera sp001679925	76.6935	180	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	76.6705	176	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058035.1	s__JAAKGP01 sp018058035	76.5547	189	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654855.1	s__JAATGA01 sp015654855	75.8979	110	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAATGA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 01:25:20,687] [INFO] GTDB search result was written to OceanDNA-b29397/result_gtdb.tsv
[2023-03-17 01:25:20,687] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:25:20,689] [INFO] DFAST_QC result json was written to OceanDNA-b29397/dqc_result.json
[2023-03-17 01:25:20,689] [INFO] DFAST_QC completed!
[2023-03-17 01:25:20,689] [INFO] Total running time: 0h1m36s