[2023-03-18 11:00:46,408] [INFO] DFAST_QC pipeline started.
[2023-03-18 11:00:46,410] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 11:00:46,410] [INFO] DQC Reference Directory: /var/lib/cwl/stgec4b9bfd-845c-401b-a2d6-cd54a01b2fba/dqc_reference
[2023-03-18 11:00:47,983] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 11:00:47,984] [INFO] Task started: Prodigal
[2023-03-18 11:00:47,984] [INFO] Running command: cat /var/lib/cwl/stg19e86bac-c69f-4c9d-b587-9e665b9e3659/OceanDNA-b35318.fa | prodigal -d OceanDNA-b35318/cds.fna -a OceanDNA-b35318/protein.faa -g 11 -q > /dev/null
[2023-03-18 11:01:17,276] [INFO] Task succeeded: Prodigal
[2023-03-18 11:01:17,277] [INFO] Task started: HMMsearch
[2023-03-18 11:01:17,277] [INFO] Running command: hmmsearch --tblout OceanDNA-b35318/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec4b9bfd-845c-401b-a2d6-cd54a01b2fba/dqc_reference/reference_markers.hmm OceanDNA-b35318/protein.faa > /dev/null
[2023-03-18 11:01:17,511] [INFO] Task succeeded: HMMsearch
[2023-03-18 11:01:17,512] [INFO] Found 6/6 markers.
[2023-03-18 11:01:17,543] [INFO] Query marker FASTA was written to OceanDNA-b35318/markers.fasta
[2023-03-18 11:01:17,544] [INFO] Task started: Blastn
[2023-03-18 11:01:17,544] [INFO] Running command: blastn -query OceanDNA-b35318/markers.fasta -db /var/lib/cwl/stgec4b9bfd-845c-401b-a2d6-cd54a01b2fba/dqc_reference/reference_markers.fasta -out OceanDNA-b35318/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 11:01:18,289] [INFO] Task succeeded: Blastn
[2023-03-18 11:01:18,298] [INFO] Selected 13 target genomes.
[2023-03-18 11:01:18,298] [INFO] Target genome list was writen to OceanDNA-b35318/target_genomes.txt
[2023-03-18 11:01:18,307] [INFO] Task started: fastANI
[2023-03-18 11:01:18,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg19e86bac-c69f-4c9d-b587-9e665b9e3659/OceanDNA-b35318.fa --refList OceanDNA-b35318/target_genomes.txt --output OceanDNA-b35318/fastani_result.tsv --threads 1
[2023-03-18 11:01:36,358] [INFO] Task succeeded: fastANI
[2023-03-18 11:01:36,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec4b9bfd-845c-401b-a2d6-cd54a01b2fba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 11:01:36,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec4b9bfd-845c-401b-a2d6-cd54a01b2fba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 11:01:36,367] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 11:01:36,367] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 11:01:36,367] [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
Vibrio chagasii	strain=CCUG 48643	GCA_008801295.1	170679	170679	suspected-type	True	93.8714	1378	1622	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	93.8572	1373	1622	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	93.8257	1412	1622	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	88.0219	1167	1622	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	87.9514	1189	1622	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	87.4714	1228	1622	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	87.0796	1173	1622	95	below_threshold
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	87.0602	1145	1622	95	below_threshold
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	85.8318	1176	1622	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	85.6682	1184	1622	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	83.1077	815	1622	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	83.005	809	1622	95	below_threshold
Vibrio profundi	strain=TP187	GCA_005281835.1	1774960	1774960	type	True	82.6414	638	1622	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 11:01:36,369] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35318/tc_result.tsv
[2023-03-18 11:01:36,373] [INFO] ===== Taxonomy check completed =====
[2023-03-18 11:01:36,373] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 11:01:36,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec4b9bfd-845c-401b-a2d6-cd54a01b2fba/dqc_reference/checkm_data
[2023-03-18 11:01:36,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 11:01:36,382] [INFO] Task started: CheckM
[2023-03-18 11:01:36,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35318/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35318/checkm_input OceanDNA-b35318/checkm_result
[2023-03-18 11:02:47,470] [INFO] Task succeeded: CheckM
[2023-03-18 11:02:47,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 11:02:47,533] [INFO] ===== Completeness check finished =====
[2023-03-18 11:02:47,533] [INFO] ===== Start GTDB Search =====
[2023-03-18 11:02:47,533] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35318/markers.fasta)
[2023-03-18 11:02:47,535] [INFO] Task started: Blastn
[2023-03-18 11:02:47,535] [INFO] Running command: blastn -query OceanDNA-b35318/markers.fasta -db /var/lib/cwl/stgec4b9bfd-845c-401b-a2d6-cd54a01b2fba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35318/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 11:02:48,771] [INFO] Task succeeded: Blastn
[2023-03-18 11:02:48,778] [INFO] Selected 12 target genomes.
[2023-03-18 11:02:48,778] [INFO] Target genome list was writen to OceanDNA-b35318/target_genomes_gtdb.txt
[2023-03-18 11:02:49,039] [INFO] Task started: fastANI
[2023-03-18 11:02:49,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg19e86bac-c69f-4c9d-b587-9e665b9e3659/OceanDNA-b35318.fa --refList OceanDNA-b35318/target_genomes_gtdb.txt --output OceanDNA-b35318/fastani_result_gtdb.tsv --threads 1
[2023-03-18 11:03:02,689] [INFO] Task succeeded: fastANI
[2023-03-18 11:03:02,697] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 11:03:02,697] [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_001635455.1	s__Vibrio sp001635455	98.6469	1510	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_002954585.1	s__Vibrio chagasii_A	95.0034	1432	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.42	95.44	0.90	0.87	4	inconclusive
GCF_005281815.1	s__Vibrio chagasii	93.8665	1372	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
GCA_000169995.1	s__Vibrio sp000169995	92.7297	1288	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156475.1	s__Vibrio gigantis	88.0219	1167	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_013394185.1	s__Vibrio sp013394185	87.6275	1204	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000316985.1	s__Vibrio sp000316985	87.3237	1106	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002875705.1	s__Vibrio sp002875705	86.9867	1120	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_000272045.2	s__Vibrio crassostreae_C	86.9257	1121	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_001557875.1	s__Vibrio splendidus_F	86.8978	1176	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_000695685.1	s__Vibrio fortis	83.2268	830	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.41	96.21	0.90	0.88	4	-
GCF_005281835.1	s__Vibrio profundi	82.6414	638	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 11:03:02,704] [INFO] GTDB search result was written to OceanDNA-b35318/result_gtdb.tsv
[2023-03-18 11:03:02,711] [INFO] ===== GTDB Search completed =====
[2023-03-18 11:03:02,716] [INFO] DFAST_QC result json was written to OceanDNA-b35318/dqc_result.json
[2023-03-18 11:03:02,716] [INFO] DFAST_QC completed!
[2023-03-18 11:03:02,716] [INFO] Total running time: 0h2m16s