[2023-03-18 07:47:43,081] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:47:43,081] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:47:43,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg96691b9d-7b0e-47ff-bb4e-ec5e2a2fb63b/dqc_reference
[2023-03-18 07:47:44,201] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:47:44,202] [INFO] Task started: Prodigal
[2023-03-18 07:47:44,202] [INFO] Running command: cat /var/lib/cwl/stg46d8aa72-953f-4398-b466-6a1a9df26b49/OceanDNA-b30157.fa | prodigal -d OceanDNA-b30157/cds.fna -a OceanDNA-b30157/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:47:58,327] [INFO] Task succeeded: Prodigal
[2023-03-18 07:47:58,327] [INFO] Task started: HMMsearch
[2023-03-18 07:47:58,327] [INFO] Running command: hmmsearch --tblout OceanDNA-b30157/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96691b9d-7b0e-47ff-bb4e-ec5e2a2fb63b/dqc_reference/reference_markers.hmm OceanDNA-b30157/protein.faa > /dev/null
[2023-03-18 07:47:58,500] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:47:58,500] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg46d8aa72-953f-4398-b466-6a1a9df26b49/OceanDNA-b30157.fa]
[2023-03-18 07:47:58,519] [INFO] Query marker FASTA was written to OceanDNA-b30157/markers.fasta
[2023-03-18 07:47:58,520] [INFO] Task started: Blastn
[2023-03-18 07:47:58,520] [INFO] Running command: blastn -query OceanDNA-b30157/markers.fasta -db /var/lib/cwl/stg96691b9d-7b0e-47ff-bb4e-ec5e2a2fb63b/dqc_reference/reference_markers.fasta -out OceanDNA-b30157/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:47:59,199] [INFO] Task succeeded: Blastn
[2023-03-18 07:47:59,200] [INFO] Selected 19 target genomes.
[2023-03-18 07:47:59,200] [INFO] Target genome list was writen to OceanDNA-b30157/target_genomes.txt
[2023-03-18 07:47:59,239] [INFO] Task started: fastANI
[2023-03-18 07:47:59,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg46d8aa72-953f-4398-b466-6a1a9df26b49/OceanDNA-b30157.fa --refList OceanDNA-b30157/target_genomes.txt --output OceanDNA-b30157/fastani_result.tsv --threads 1
[2023-03-18 07:48:09,901] [INFO] Task succeeded: fastANI
[2023-03-18 07:48:09,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96691b9d-7b0e-47ff-bb4e-ec5e2a2fb63b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:48:09,901] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96691b9d-7b0e-47ff-bb4e-ec5e2a2fb63b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:48:09,912] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:48:09,912] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:48:09,912] [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
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.8188	233	773	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	77.4206	216	773	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	77.401	213	773	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	77.0918	112	773	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	77.0498	171	773	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.0164	163	773	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.0162	163	773	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	77.0027	147	773	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.9253	124	773	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	76.8632	169	773	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	76.8499	171	773	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	76.835	139	773	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	76.7568	139	773	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	76.7419	140	773	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	76.7379	139	773	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	76.7221	151	773	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.6915	145	773	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.6915	145	773	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	76.4754	149	773	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:48:09,913] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30157/tc_result.tsv
[2023-03-18 07:48:09,913] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:48:09,913] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:48:09,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96691b9d-7b0e-47ff-bb4e-ec5e2a2fb63b/dqc_reference/checkm_data
[2023-03-18 07:48:09,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:48:09,918] [INFO] Task started: CheckM
[2023-03-18 07:48:09,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30157/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30157/checkm_input OceanDNA-b30157/checkm_result
[2023-03-18 07:48:48,155] [INFO] Task succeeded: CheckM
[2023-03-18 07:48:48,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.92%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:48:48,158] [INFO] ===== Completeness check finished =====
[2023-03-18 07:48:48,158] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:48:48,158] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30157/markers.fasta)
[2023-03-18 07:48:48,159] [INFO] Task started: Blastn
[2023-03-18 07:48:48,159] [INFO] Running command: blastn -query OceanDNA-b30157/markers.fasta -db /var/lib/cwl/stg96691b9d-7b0e-47ff-bb4e-ec5e2a2fb63b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30157/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:48:49,265] [INFO] Task succeeded: Blastn
[2023-03-18 07:48:49,266] [INFO] Selected 23 target genomes.
[2023-03-18 07:48:49,266] [INFO] Target genome list was writen to OceanDNA-b30157/target_genomes_gtdb.txt
[2023-03-18 07:48:49,692] [INFO] Task started: fastANI
[2023-03-18 07:48:49,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg46d8aa72-953f-4398-b466-6a1a9df26b49/OceanDNA-b30157.fa --refList OceanDNA-b30157/target_genomes_gtdb.txt --output OceanDNA-b30157/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:49:04,288] [INFO] Task succeeded: fastANI
[2023-03-18 07:49:04,302] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:49:04,302] [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_009830125.1	s__GH1-50 sp009830125	77.832	232	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148765.1	s__Silicimonas algicola	77.4206	216	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015689745.1	s__Roseicyclus sp015689745	77.2614	165	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002465.1	s__JABDJO01 sp013002465	77.1811	185	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	77.1578	157	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	77.1147	190	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.0475	161	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCA_013042605.1	s__IMCC34051 sp013042605	77.026	146	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	99.10	98.86	0.88	0.86	4	-
GCA_011620265.1	s__Albidovulum sp011620265	77.019	156	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	76.9952	181	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116005.1	s__Poseidonocella sedimentorum	76.9374	135	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	76.9253	124	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCA_008933605.1	s__Albidovulum sp008933605	76.793	109	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003245.1	s__JABDJX01 sp013003245	76.7591	125	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	76.758	164	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908165.1	s__Frigidibacter albus	76.7558	139	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	100.00	100.00	1.00	0.99	4	-
GCF_003129565.1	s__Salibaculum griseiflavum	76.7221	151	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424695.1	s__Vannielia litorea_A	76.7124	140	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112685.1	s__Roseivivax sediminis	76.7025	169	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	76.6755	146	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002440625.1	s__Albidovulum sp002440625	76.6751	100	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003428585.1	s__Nioella sp003428585	76.5735	135	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172265.1	s__Roseivivax jejudonensis	76.4897	148	773	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:49:04,302] [INFO] GTDB search result was written to OceanDNA-b30157/result_gtdb.tsv
[2023-03-18 07:49:04,302] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:49:04,305] [INFO] DFAST_QC result json was written to OceanDNA-b30157/dqc_result.json
[2023-03-18 07:49:04,305] [INFO] DFAST_QC completed!
[2023-03-18 07:49:04,305] [INFO] Total running time: 0h1m21s