[2023-03-18 04:16:53,143] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:53,143] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:53,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg3174a94f-5273-446f-af18-e942e5787dd7/dqc_reference
[2023-03-18 04:16:54,279] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:54,279] [INFO] Task started: Prodigal
[2023-03-18 04:16:54,280] [INFO] Running command: cat /var/lib/cwl/stgf4995203-6055-485e-9b05-2e4c3c299ae6/OceanDNA-b36144.fa | prodigal -d OceanDNA-b36144/cds.fna -a OceanDNA-b36144/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:17:15,548] [INFO] Task succeeded: Prodigal
[2023-03-18 04:17:15,548] [INFO] Task started: HMMsearch
[2023-03-18 04:17:15,548] [INFO] Running command: hmmsearch --tblout OceanDNA-b36144/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3174a94f-5273-446f-af18-e942e5787dd7/dqc_reference/reference_markers.hmm OceanDNA-b36144/protein.faa > /dev/null
[2023-03-18 04:17:15,745] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:17:15,746] [INFO] Found 6/6 markers.
[2023-03-18 04:17:15,764] [INFO] Query marker FASTA was written to OceanDNA-b36144/markers.fasta
[2023-03-18 04:17:15,765] [INFO] Task started: Blastn
[2023-03-18 04:17:15,765] [INFO] Running command: blastn -query OceanDNA-b36144/markers.fasta -db /var/lib/cwl/stg3174a94f-5273-446f-af18-e942e5787dd7/dqc_reference/reference_markers.fasta -out OceanDNA-b36144/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:16,558] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:16,559] [INFO] Selected 29 target genomes.
[2023-03-18 04:17:16,559] [INFO] Target genome list was writen to OceanDNA-b36144/target_genomes.txt
[2023-03-18 04:17:16,578] [INFO] Task started: fastANI
[2023-03-18 04:17:16,579] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4995203-6055-485e-9b05-2e4c3c299ae6/OceanDNA-b36144.fa --refList OceanDNA-b36144/target_genomes.txt --output OceanDNA-b36144/fastani_result.tsv --threads 1
[2023-03-18 04:17:33,652] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:33,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3174a94f-5273-446f-af18-e942e5787dd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:33,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3174a94f-5273-446f-af18-e942e5787dd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:33,667] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:17:33,667] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:17:33,667] [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
Abyssibacter profundi	strain=OUC007	GCA_003151135.1	2182787	2182787	type	True	79.525	524	1110	95	below_threshold
Oceanococcus atlanticus	strain=22II-S10r2	GCA_002088235.1	1317117	1317117	type	True	77.08	100	1110	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	76.873	57	1110	95	below_threshold
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	76.472	64	1110	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	76.3752	68	1110	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	76.3515	121	1110	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	76.256	139	1110	95	below_threshold
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	76.2245	109	1110	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	76.2231	152	1110	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	76.1922	50	1110	95	below_threshold
Polycyclovorans algicola	strain=TG408	GCA_000711245.1	616992	616992	type	True	76.1324	83	1110	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	76.1206	111	1110	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	76.0785	116	1110	95	below_threshold
Halochromatium roseum	strain=DSM 18859	GCA_016653315.1	391920	391920	type	True	76.0447	52	1110	95	below_threshold
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	76.0157	136	1110	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.0051	71	1110	95	below_threshold
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	75.9842	80	1110	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	75.8433	62	1110	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	75.8283	56	1110	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	75.7958	85	1110	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	75.7514	83	1110	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	75.7246	85	1110	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	75.5491	75	1110	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	75.4518	72	1110	95	below_threshold
Pseudomonas chlororaphis subsp. chlororaphis	strain=LMG 5004	GCA_001269625.1	333	587753	type	True	75.4288	73	1110	95	below_threshold
Pseudomonas chlororaphis subsp. chlororaphis	strain=DSM 50083	GCA_007858335.1	333	587753	type	True	75.4262	73	1110	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:17:33,667] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36144/tc_result.tsv
[2023-03-18 04:17:33,667] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:33,667] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:33,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3174a94f-5273-446f-af18-e942e5787dd7/dqc_reference/checkm_data
[2023-03-18 04:17:33,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:33,814] [INFO] Task started: CheckM
[2023-03-18 04:17:33,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36144/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36144/checkm_input OceanDNA-b36144/checkm_result
[2023-03-18 04:18:27,972] [INFO] Task succeeded: CheckM
[2023-03-18 04:18:27,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:18:27,974] [INFO] ===== Completeness check finished =====
[2023-03-18 04:18:27,974] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:18:27,975] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36144/markers.fasta)
[2023-03-18 04:18:27,976] [INFO] Task started: Blastn
[2023-03-18 04:18:27,976] [INFO] Running command: blastn -query OceanDNA-b36144/markers.fasta -db /var/lib/cwl/stg3174a94f-5273-446f-af18-e942e5787dd7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36144/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:18:29,440] [INFO] Task succeeded: Blastn
[2023-03-18 04:18:29,441] [INFO] Selected 29 target genomes.
[2023-03-18 04:18:29,441] [INFO] Target genome list was writen to OceanDNA-b36144/target_genomes_gtdb.txt
[2023-03-18 04:18:29,764] [INFO] Task started: fastANI
[2023-03-18 04:18:29,765] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4995203-6055-485e-9b05-2e4c3c299ae6/OceanDNA-b36144.fa --refList OceanDNA-b36144/target_genomes_gtdb.txt --output OceanDNA-b36144/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:18:46,014] [INFO] Task succeeded: fastANI
[2023-03-18 04:18:46,027] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:18:46,028] [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_003151135.1	s__Abyssibacter profundi	79.5337	523	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__OUC007;g__Abyssibacter	95.0	98.39	98.39	0.93	0.93	2	-
GCA_018222345.1	s__JAAFAL01 sp018222345	77.6072	147	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__OUC007;g__JAAFAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088235.1	s__Oceanococcus atlanticus	77.08	100	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Oceanococcaceae;g__Oceanococcus	95.0	98.37	98.37	0.93	0.93	2	-
GCF_000378305.1	s__Thioalkalivibrio sp000378305	76.637	56	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	98.92	98.55	0.95	0.94	12	-
GCF_000377785.1	s__Thioalkalivibrio sp000377785	76.6196	62	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699185.1	s__Thiohalobacter sp002699185	76.5391	54	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381945.1	s__Thioalkalivibrio sp000381945	76.3842	67	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025545.1	s__Thioalkalivibrio sp000025545	76.3679	64	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.34	97.34	0.93	0.93	2	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	76.3648	120	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012115.1	s__Stenotrophobium sp008012115	76.3062	107	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382285.1	s__Solimonas variicoloris	76.2231	152	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000429605.1	s__Azonexus hydrophilus	76.1922	50	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.24	97.24	0.86	0.86	2	-
GCF_000711245.1	s__Polycyclovorans algicola	76.1324	83	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126095.1	s__Aquisalimonas sp007126095	76.0931	56	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	99.75	99.73	0.94	0.94	3	-
GCF_003788635.1	s__Salinisphaera orenii	76.0785	116	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_016653315.1	s__Halochromatium roseum	76.0447	52	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711955.1	s__Nevskia soli	76.0223	134	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822975.1	s__Nevskia sp903822975	75.991	78	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000215955.2	s__Salinisphaera shabanensis	75.9842	80	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182845.1	s__JACPFT01 sp016182845	75.9746	63	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__DSM-103792;g__JACPFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018599185.1	s__Rhodanobacter sp018599185	75.9626	74	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011064545.1	s__XN24 sp011064545	75.9402	63	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634965.1	s__Azonexus fungiphilus	75.8433	62	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.36	98.36	0.85	0.85	2	-
GCF_016583905.1	s__Halochromatium modestohalophilus	75.8153	50	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584105.1	s__Ectothiorhodospira shaposhnikovii	75.5848	54	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:18:46,028] [INFO] GTDB search result was written to OceanDNA-b36144/result_gtdb.tsv
[2023-03-18 04:18:46,028] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:18:46,030] [INFO] DFAST_QC result json was written to OceanDNA-b36144/dqc_result.json
[2023-03-18 04:18:46,030] [INFO] DFAST_QC completed!
[2023-03-18 04:18:46,030] [INFO] Total running time: 0h1m53s