[2023-03-17 04:15:16,730] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:16,730] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:16,730] [INFO] DQC Reference Directory: /var/lib/cwl/stge3a33340-dd68-482e-849f-6cd047e0b42c/dqc_reference
[2023-03-17 04:15:17,998] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:17,998] [INFO] Task started: Prodigal
[2023-03-17 04:15:17,998] [INFO] Running command: cat /var/lib/cwl/stga54fc07c-3d00-416e-b9d9-7f9923019a1a/OceanDNA-b6639.fa | prodigal -d OceanDNA-b6639/cds.fna -a OceanDNA-b6639/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:41,021] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:41,022] [INFO] Task started: HMMsearch
[2023-03-17 04:15:41,022] [INFO] Running command: hmmsearch --tblout OceanDNA-b6639/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3a33340-dd68-482e-849f-6cd047e0b42c/dqc_reference/reference_markers.hmm OceanDNA-b6639/protein.faa > /dev/null
[2023-03-17 04:15:41,243] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:41,243] [INFO] Found 6/6 markers.
[2023-03-17 04:15:41,264] [INFO] Query marker FASTA was written to OceanDNA-b6639/markers.fasta
[2023-03-17 04:15:41,265] [INFO] Task started: Blastn
[2023-03-17 04:15:41,265] [INFO] Running command: blastn -query OceanDNA-b6639/markers.fasta -db /var/lib/cwl/stge3a33340-dd68-482e-849f-6cd047e0b42c/dqc_reference/reference_markers.fasta -out OceanDNA-b6639/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:41,826] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:41,827] [INFO] Selected 27 target genomes.
[2023-03-17 04:15:41,827] [INFO] Target genome list was writen to OceanDNA-b6639/target_genomes.txt
[2023-03-17 04:15:41,838] [INFO] Task started: fastANI
[2023-03-17 04:15:41,838] [INFO] Running command: fastANI --query /var/lib/cwl/stga54fc07c-3d00-416e-b9d9-7f9923019a1a/OceanDNA-b6639.fa --refList OceanDNA-b6639/target_genomes.txt --output OceanDNA-b6639/fastani_result.tsv --threads 1
[2023-03-17 04:15:57,774] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:57,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3a33340-dd68-482e-849f-6cd047e0b42c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:57,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3a33340-dd68-482e-849f-6cd047e0b42c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:57,786] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:57,786] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:15:57,786] [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	78.7504	123	1026	95	below_threshold
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	77.5918	116	1026	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	77.5717	134	1026	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	77.5179	260	1026	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	76.9484	108	1026	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	76.904	65	1026	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.8945	83	1026	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.8528	63	1026	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	76.7656	113	1026	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	76.7469	51	1026	95	below_threshold
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	76.7254	99	1026	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.6809	130	1026	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.6338	135	1026	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.6328	58	1026	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.6163	135	1026	95	below_threshold
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	76.5268	62	1026	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	76.4177	66	1026	95	below_threshold
Snuella sedimenti	strain=CAU 1569	GCA_016428595.1	2798802	2798802	type	True	76.2912	55	1026	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	76.2651	61	1026	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:57,786] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6639/tc_result.tsv
[2023-03-17 04:15:57,786] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:57,786] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:57,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3a33340-dd68-482e-849f-6cd047e0b42c/dqc_reference/checkm_data
[2023-03-17 04:15:57,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:57,792] [INFO] Task started: CheckM
[2023-03-17 04:15:57,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6639/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6639/checkm_input OceanDNA-b6639/checkm_result
[2023-03-17 04:16:55,316] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:55,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:55,319] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:55,319] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:55,319] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6639/markers.fasta)
[2023-03-17 04:16:55,319] [INFO] Task started: Blastn
[2023-03-17 04:16:55,319] [INFO] Running command: blastn -query OceanDNA-b6639/markers.fasta -db /var/lib/cwl/stge3a33340-dd68-482e-849f-6cd047e0b42c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6639/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:56,099] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:56,100] [INFO] Selected 23 target genomes.
[2023-03-17 04:16:56,100] [INFO] Target genome list was writen to OceanDNA-b6639/target_genomes_gtdb.txt
[2023-03-17 04:16:56,488] [INFO] Task started: fastANI
[2023-03-17 04:16:56,488] [INFO] Running command: fastANI --query /var/lib/cwl/stga54fc07c-3d00-416e-b9d9-7f9923019a1a/OceanDNA-b6639.fa --refList OceanDNA-b6639/target_genomes_gtdb.txt --output OceanDNA-b6639/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:17:08,365] [INFO] Task succeeded: fastANI
[2023-03-17 04:17:08,375] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:17:08,375] [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_002707025.1	s__IN17 sp002707025	99.8385	977	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.83	99.78	0.96	0.93	3	conclusive
GCF_000746845.1	s__Altibacter lentus	78.7864	122	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694465.1	s__IN17 sp002694465	78.0199	270	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
GCA_002631855.1	s__Marixanthomonas sp002631855	77.6089	141	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	77.5717	134	1026	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	77.4779	158	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCA_002375495.1	s__Marinirhabdus sp002375495	77.4759	136	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCF_014641635.1	s__Aquaticitalea lipolytica	77.3407	50	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364245.1	s__Marixanthomonas sp002364245	77.303	92	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002065.1	s__SMXJ01 sp013002065	77.2723	119	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011044175.1	s__Marinirhabdus sp011044175	77.1655	111	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002379985.1	s__Marixanthomonas sp002379985	76.9562	99	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	99.95	99.94	0.93	0.86	4	-
GCF_002813135.1	s__Altibacter sp002813135	76.939	116	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440705.1	s__IN17 sp002440705	76.924	197	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.92	99.92	0.93	0.93	2	-
GCF_003095375.1	s__Marixanthomonas sp003095375	76.6809	130	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	76.6457	106	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	76.6327	134	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_019090365.1	s__GCA-002733185 sp019090365	75.454	55	1026	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:17:08,375] [INFO] GTDB search result was written to OceanDNA-b6639/result_gtdb.tsv
[2023-03-17 04:17:08,375] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:17:08,377] [INFO] DFAST_QC result json was written to OceanDNA-b6639/dqc_result.json
[2023-03-17 04:17:08,377] [INFO] DFAST_QC completed!
[2023-03-17 04:17:08,377] [INFO] Total running time: 0h1m52s