[2023-03-15 11:09:10,829] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,829] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,829] [INFO] DQC Reference Directory: /var/lib/cwl/stg95f41d87-c5f5-4c11-bbde-698622028168/dqc_reference
[2023-03-15 11:09:12,141] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,141] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,141] [INFO] Running command: cat /var/lib/cwl/stg94c88b43-4790-4485-9f7f-d2f238a9facb/OceanDNA-b9715.fa | prodigal -d OceanDNA-b9715/cds.fna -a OceanDNA-b9715/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:30,708] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:30,708] [INFO] Task started: HMMsearch
[2023-03-15 11:09:30,708] [INFO] Running command: hmmsearch --tblout OceanDNA-b9715/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95f41d87-c5f5-4c11-bbde-698622028168/dqc_reference/reference_markers.hmm OceanDNA-b9715/protein.faa > /dev/null
[2023-03-15 11:09:30,958] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:30,959] [INFO] Found 6/6 markers.
[2023-03-15 11:09:30,979] [INFO] Query marker FASTA was written to OceanDNA-b9715/markers.fasta
[2023-03-15 11:09:30,979] [INFO] Task started: Blastn
[2023-03-15 11:09:30,979] [INFO] Running command: blastn -query OceanDNA-b9715/markers.fasta -db /var/lib/cwl/stg95f41d87-c5f5-4c11-bbde-698622028168/dqc_reference/reference_markers.fasta -out OceanDNA-b9715/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:31,585] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:31,586] [INFO] Selected 18 target genomes.
[2023-03-15 11:09:31,586] [INFO] Target genome list was writen to OceanDNA-b9715/target_genomes.txt
[2023-03-15 11:09:31,596] [INFO] Task started: fastANI
[2023-03-15 11:09:31,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg94c88b43-4790-4485-9f7f-d2f238a9facb/OceanDNA-b9715.fa --refList OceanDNA-b9715/target_genomes.txt --output OceanDNA-b9715/fastani_result.tsv --threads 1
[2023-03-15 11:09:42,705] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:42,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95f41d87-c5f5-4c11-bbde-698622028168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:42,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95f41d87-c5f5-4c11-bbde-698622028168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:42,716] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:42,716] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:42,716] [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
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	85.2051	764	908	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	80.2355	590	908	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	77.3382	225	908	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.3358	226	908	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.0286	198	908	95	below_threshold
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	76.9884	142	908	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	76.9552	120	908	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.8058	69	908	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.8005	163	908	95	below_threshold
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	76.7749	144	908	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	76.6981	126	908	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	76.6856	125	908	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	76.6047	95	908	95	below_threshold
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	76.5264	136	908	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.5113	73	908	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.331	98	908	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.3255	82	908	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	75.8897	57	908	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:42,716] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9715/tc_result.tsv
[2023-03-15 11:09:42,717] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:42,717] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:42,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95f41d87-c5f5-4c11-bbde-698622028168/dqc_reference/checkm_data
[2023-03-15 11:09:42,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:42,722] [INFO] Task started: CheckM
[2023-03-15 11:09:42,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9715/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9715/checkm_input OceanDNA-b9715/checkm_result
[2023-03-15 11:10:30,505] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:30,506] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:30,688] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:30,688] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:30,689] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9715/markers.fasta)
[2023-03-15 11:10:30,689] [INFO] Task started: Blastn
[2023-03-15 11:10:30,689] [INFO] Running command: blastn -query OceanDNA-b9715/markers.fasta -db /var/lib/cwl/stg95f41d87-c5f5-4c11-bbde-698622028168/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9715/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:31,539] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:31,540] [INFO] Selected 10 target genomes.
[2023-03-15 11:10:31,540] [INFO] Target genome list was writen to OceanDNA-b9715/target_genomes_gtdb.txt
[2023-03-15 11:10:31,550] [INFO] Task started: fastANI
[2023-03-15 11:10:31,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg94c88b43-4790-4485-9f7f-d2f238a9facb/OceanDNA-b9715.fa --refList OceanDNA-b9715/target_genomes_gtdb.txt --output OceanDNA-b9715/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:38,028] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:38,034] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:10:38,034] [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_002364245.1	s__Marixanthomonas sp002364245	99.7905	537	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002631855.1	s__Marixanthomonas sp002631855	94.2765	806	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360635.1	s__Marixanthomonas sp002360635	90.495	777	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCF_003413745.1	s__Marixanthomonas ophiurae	85.2051	764	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003095375.1	s__Marixanthomonas sp003095375	80.2449	589	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	77.3382	225	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002337605.1	s__Marinirhabdus sp002337605	77.2639	197	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.69	98.69	0.95	0.95	2	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	77.0286	198	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011044175.1	s__Marinirhabdus sp011044175	77.0258	160	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016827595.1	s__Marixanthomonas sp016827595	76.7321	149	908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:38,035] [INFO] GTDB search result was written to OceanDNA-b9715/result_gtdb.tsv
[2023-03-15 11:10:38,035] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:38,036] [INFO] DFAST_QC result json was written to OceanDNA-b9715/dqc_result.json
[2023-03-15 11:10:38,036] [INFO] DFAST_QC completed!
[2023-03-15 11:10:38,036] [INFO] Total running time: 0h1m27s