[2023-03-15 21:48:06,738] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:06,738] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:06,738] [INFO] DQC Reference Directory: /var/lib/cwl/stgb782cbab-f378-4b8b-a6af-993131bb6942/dqc_reference
[2023-03-15 21:48:07,866] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:07,867] [INFO] Task started: Prodigal
[2023-03-15 21:48:07,867] [INFO] Running command: cat /var/lib/cwl/stg85eb24b9-b796-4dc0-94bc-44cee50c9d88/OceanDNA-b10734.fa | prodigal -d OceanDNA-b10734/cds.fna -a OceanDNA-b10734/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:29,509] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:29,510] [INFO] Task started: HMMsearch
[2023-03-15 21:48:29,510] [INFO] Running command: hmmsearch --tblout OceanDNA-b10734/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb782cbab-f378-4b8b-a6af-993131bb6942/dqc_reference/reference_markers.hmm OceanDNA-b10734/protein.faa > /dev/null
[2023-03-15 21:48:29,707] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:29,707] [INFO] Found 6/6 markers.
[2023-03-15 21:48:29,725] [INFO] Query marker FASTA was written to OceanDNA-b10734/markers.fasta
[2023-03-15 21:48:29,726] [INFO] Task started: Blastn
[2023-03-15 21:48:29,727] [INFO] Running command: blastn -query OceanDNA-b10734/markers.fasta -db /var/lib/cwl/stgb782cbab-f378-4b8b-a6af-993131bb6942/dqc_reference/reference_markers.fasta -out OceanDNA-b10734/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:30,290] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:30,291] [INFO] Selected 24 target genomes.
[2023-03-15 21:48:30,291] [INFO] Target genome list was writen to OceanDNA-b10734/target_genomes.txt
[2023-03-15 21:48:30,306] [INFO] Task started: fastANI
[2023-03-15 21:48:30,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg85eb24b9-b796-4dc0-94bc-44cee50c9d88/OceanDNA-b10734.fa --refList OceanDNA-b10734/target_genomes.txt --output OceanDNA-b10734/fastani_result.tsv --threads 1
[2023-03-15 21:48:43,348] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:43,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb782cbab-f378-4b8b-a6af-993131bb6942/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:43,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb782cbab-f378-4b8b-a6af-993131bb6942/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:43,357] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:43,357] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:48:43,357] [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
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	77.0493	107	942	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.6407	93	942	95	below_threshold
Aureitalea marina	strain=NBRC 107741	GCA_002943755.1	930804	930804	type	True	76.5729	59	942	95	below_threshold
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	76.5574	94	942	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.4702	104	942	95	below_threshold
Luteirhabdus pelagi	strain=A3-108	GCA_016827595.1	2792783	2792783	type	True	76.4208	103	942	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	76.2556	105	942	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	76.2041	71	942	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	76.1637	69	942	95	below_threshold
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	76.112	61	942	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	75.9533	65	942	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	75.8967	77	942	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	75.7092	66	942	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:48:43,359] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10734/tc_result.tsv
[2023-03-15 21:48:43,359] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:43,359] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:43,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb782cbab-f378-4b8b-a6af-993131bb6942/dqc_reference/checkm_data
[2023-03-15 21:48:43,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:43,365] [INFO] Task started: CheckM
[2023-03-15 21:48:43,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10734/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10734/checkm_input OceanDNA-b10734/checkm_result
[2023-03-15 21:49:38,833] [INFO] Task succeeded: CheckM
[2023-03-15 21:49:38,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:49:38,850] [INFO] ===== Completeness check finished =====
[2023-03-15 21:49:38,850] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:49:38,850] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10734/markers.fasta)
[2023-03-15 21:49:38,851] [INFO] Task started: Blastn
[2023-03-15 21:49:38,851] [INFO] Running command: blastn -query OceanDNA-b10734/markers.fasta -db /var/lib/cwl/stgb782cbab-f378-4b8b-a6af-993131bb6942/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10734/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:49:39,628] [INFO] Task succeeded: Blastn
[2023-03-15 21:49:39,633] [INFO] Selected 25 target genomes.
[2023-03-15 21:49:39,633] [INFO] Target genome list was writen to OceanDNA-b10734/target_genomes_gtdb.txt
[2023-03-15 21:49:39,753] [INFO] Task started: fastANI
[2023-03-15 21:49:39,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg85eb24b9-b796-4dc0-94bc-44cee50c9d88/OceanDNA-b10734.fa --refList OceanDNA-b10734/target_genomes_gtdb.txt --output OceanDNA-b10734/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:49:54,886] [INFO] Task succeeded: fastANI
[2023-03-15 21:49:54,896] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:49:54,896] [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_002379985.1	s__Marixanthomonas sp002379985	99.9558	886	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	99.95	99.94	0.93	0.86	4	conclusive
GCF_000746845.1	s__Altibacter lentus	77.0247	108	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008501705.1	s__Pukyongia sp008501705	76.6605	87	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707025.1	s__IN17 sp002707025	76.5936	111	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.83	99.78	0.96	0.93	3	-
GCF_002966125.1	s__Pukyongia salina	76.5574	94	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375495.1	s__Marinirhabdus sp002375495	76.4875	111	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCA_002337605.1	s__Marinirhabdus sp002337605	76.4332	98	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.69	98.69	0.95	0.95	2	-
GCF_016827595.1	s__Marixanthomonas sp016827595	76.4174	103	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364245.1	s__Marixanthomonas sp002364245	76.3334	72	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440705.1	s__IN17 sp002440705	76.2991	60	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.92	99.92	0.93	0.93	2	-
GCA_002631855.1	s__Marixanthomonas sp002631855	76.2976	117	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014295415.1	s__Altibacter sp014295415	76.2556	105	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001573155.1	s__Aequorivita aquimaris	76.1788	72	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	76.1637	69	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCA_905479745.1	s__Pukyongia sp905479745	76.1396	74	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018476645.1	s__Aequorivita echinoideorum	76.0841	62	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346335.1	s__Aequorivita sinensis	75.7092	66	942	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-15 21:49:54,897] [INFO] GTDB search result was written to OceanDNA-b10734/result_gtdb.tsv
[2023-03-15 21:49:54,897] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:49:54,899] [INFO] DFAST_QC result json was written to OceanDNA-b10734/dqc_result.json
[2023-03-15 21:49:54,899] [INFO] DFAST_QC completed!
[2023-03-15 21:49:54,900] [INFO] Total running time: 0h1m48s