[2023-03-18 22:24:43,962] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:24:43,963] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:24:43,963] [INFO] DQC Reference Directory: /var/lib/cwl/stg119a47fc-6605-4b0f-9f99-83d9f70f39d9/dqc_reference
[2023-03-18 22:24:45,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:24:45,074] [INFO] Task started: Prodigal
[2023-03-18 22:24:45,074] [INFO] Running command: cat /var/lib/cwl/stg972ebd73-2be0-4c55-b124-0bf7b38bb9b3/OceanDNA-b11345.fa | prodigal -d OceanDNA-b11345/cds.fna -a OceanDNA-b11345/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:25:03,149] [INFO] Task succeeded: Prodigal
[2023-03-18 22:25:03,150] [INFO] Task started: HMMsearch
[2023-03-18 22:25:03,150] [INFO] Running command: hmmsearch --tblout OceanDNA-b11345/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg119a47fc-6605-4b0f-9f99-83d9f70f39d9/dqc_reference/reference_markers.hmm OceanDNA-b11345/protein.faa > /dev/null
[2023-03-18 22:25:03,345] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:25:03,345] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg972ebd73-2be0-4c55-b124-0bf7b38bb9b3/OceanDNA-b11345.fa]
[2023-03-18 22:25:03,363] [INFO] Query marker FASTA was written to OceanDNA-b11345/markers.fasta
[2023-03-18 22:25:03,364] [INFO] Task started: Blastn
[2023-03-18 22:25:03,364] [INFO] Running command: blastn -query OceanDNA-b11345/markers.fasta -db /var/lib/cwl/stg119a47fc-6605-4b0f-9f99-83d9f70f39d9/dqc_reference/reference_markers.fasta -out OceanDNA-b11345/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:25:03,895] [INFO] Task succeeded: Blastn
[2023-03-18 22:25:03,896] [INFO] Selected 18 target genomes.
[2023-03-18 22:25:03,896] [INFO] Target genome list was writen to OceanDNA-b11345/target_genomes.txt
[2023-03-18 22:25:03,906] [INFO] Task started: fastANI
[2023-03-18 22:25:03,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg972ebd73-2be0-4c55-b124-0bf7b38bb9b3/OceanDNA-b11345.fa --refList OceanDNA-b11345/target_genomes.txt --output OceanDNA-b11345/fastani_result.tsv --threads 1
[2023-03-18 22:25:14,187] [INFO] Task succeeded: fastANI
[2023-03-18 22:25:14,187] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg119a47fc-6605-4b0f-9f99-83d9f70f39d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:25:14,187] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg119a47fc-6605-4b0f-9f99-83d9f70f39d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:25:14,196] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:25:14,196] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:25:14,196] [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
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.1449	188	915	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	77.1419	189	915	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	77.0406	164	915	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	76.4982	74	915	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	76.2306	77	915	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	76.009	96	915	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	75.9899	57	915	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	75.8885	64	915	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	75.6913	51	915	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	75.6885	71	915	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	75.5531	57	915	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	75.5169	61	915	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	75.4789	68	915	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:25:14,196] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11345/tc_result.tsv
[2023-03-18 22:25:14,196] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:25:14,196] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:25:14,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg119a47fc-6605-4b0f-9f99-83d9f70f39d9/dqc_reference/checkm_data
[2023-03-18 22:25:14,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:25:14,202] [INFO] Task started: CheckM
[2023-03-18 22:25:14,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11345/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11345/checkm_input OceanDNA-b11345/checkm_result
[2023-03-18 22:26:01,633] [INFO] Task succeeded: CheckM
[2023-03-18 22:26:01,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:26:01,636] [INFO] ===== Completeness check finished =====
[2023-03-18 22:26:01,636] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:26:01,636] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11345/markers.fasta)
[2023-03-18 22:26:01,637] [INFO] Task started: Blastn
[2023-03-18 22:26:01,637] [INFO] Running command: blastn -query OceanDNA-b11345/markers.fasta -db /var/lib/cwl/stg119a47fc-6605-4b0f-9f99-83d9f70f39d9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11345/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:26:02,384] [INFO] Task succeeded: Blastn
[2023-03-18 22:26:02,385] [INFO] Selected 20 target genomes.
[2023-03-18 22:26:02,385] [INFO] Target genome list was writen to OceanDNA-b11345/target_genomes_gtdb.txt
[2023-03-18 22:26:02,406] [INFO] Task started: fastANI
[2023-03-18 22:26:02,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg972ebd73-2be0-4c55-b124-0bf7b38bb9b3/OceanDNA-b11345.fa --refList OceanDNA-b11345/target_genomes_gtdb.txt --output OceanDNA-b11345/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:26:12,980] [INFO] Task succeeded: fastANI
[2023-03-18 22:26:12,990] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:26:12,990] [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_900102055.1	s__Ulvibacter litoralis	77.1419	189	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003688405.1	s__Ulvibacter antarcticus	77.0406	164	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018669795.1	s__GCA-002733185 sp018669795	76.4912	73	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	98.54	95.82	0.94	0.91	4	-
GCF_001641085.1	s__Aequorivita soesokkakensis	76.2092	78	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCA_002364245.1	s__Marixanthomonas sp002364245	76.1394	64	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974325.1	s__Patiriisocius marinus	76.009	96	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	75.9899	57	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCA_002733915.1	s__Aequorivita sp002733915	75.8848	60	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713705.1	s__GCA-002733185 sp002713705	75.8582	75	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	97.32	97.11	0.93	0.92	3	-
GCF_011777505.1	s__CAU-1491 sp011777505	75.6953	51	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518485.1	s__Olleya marilimosa	75.6913	51	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_001418105.1	s__Oceanihabitans himadriensis	75.6885	71	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	75.6693	61	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	75.6463	57	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCA_905181835.1	s__GCA-002733185 sp905181835	75.5746	55	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429125.1	s__Aequorivita capsosiphonis	75.4789	68	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827365.1	s__Olleya sp002323495	75.4204	51	915	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:26:12,990] [INFO] GTDB search result was written to OceanDNA-b11345/result_gtdb.tsv
[2023-03-18 22:26:12,990] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:26:12,993] [INFO] DFAST_QC result json was written to OceanDNA-b11345/dqc_result.json
[2023-03-18 22:26:12,993] [INFO] DFAST_QC completed!
[2023-03-18 22:26:12,993] [INFO] Total running time: 0h1m29s