[2023-03-19 04:11:06,922] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg95cf4f56-29b2-401f-ae6d-1d3570d95fc8/dqc_reference
[2023-03-19 04:11:08,543] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,544] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,544] [INFO] Running command: cat /var/lib/cwl/stg491ed4d8-c7b3-4e74-9c7f-e951d6fe91e4/OceanDNA-b37527.fa | prodigal -d OceanDNA-b37527/cds.fna -a OceanDNA-b37527/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:30,065] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:30,065] [INFO] Task started: HMMsearch
[2023-03-19 04:11:30,065] [INFO] Running command: hmmsearch --tblout OceanDNA-b37527/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95cf4f56-29b2-401f-ae6d-1d3570d95fc8/dqc_reference/reference_markers.hmm OceanDNA-b37527/protein.faa > /dev/null
[2023-03-19 04:11:30,266] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:30,266] [INFO] Found 6/6 markers.
[2023-03-19 04:11:30,287] [INFO] Query marker FASTA was written to OceanDNA-b37527/markers.fasta
[2023-03-19 04:11:30,288] [INFO] Task started: Blastn
[2023-03-19 04:11:30,288] [INFO] Running command: blastn -query OceanDNA-b37527/markers.fasta -db /var/lib/cwl/stg95cf4f56-29b2-401f-ae6d-1d3570d95fc8/dqc_reference/reference_markers.fasta -out OceanDNA-b37527/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:31,000] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:31,001] [INFO] Selected 27 target genomes.
[2023-03-19 04:11:31,002] [INFO] Target genome list was writen to OceanDNA-b37527/target_genomes.txt
[2023-03-19 04:11:31,014] [INFO] Task started: fastANI
[2023-03-19 04:11:31,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg491ed4d8-c7b3-4e74-9c7f-e951d6fe91e4/OceanDNA-b37527.fa --refList OceanDNA-b37527/target_genomes.txt --output OceanDNA-b37527/fastani_result.tsv --threads 1
[2023-03-19 04:11:47,592] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:47,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95cf4f56-29b2-401f-ae6d-1d3570d95fc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:47,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95cf4f56-29b2-401f-ae6d-1d3570d95fc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:47,606] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:47,607] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:11:47,607] [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
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.6942	243	1141	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.4691	186	1141	95	below_threshold
Congregibacter litoralis	strain=KT71	GCA_000153125.2	393662	393662	type	True	77.1483	242	1141	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.0629	194	1141	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.9708	220	1141	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	76.9498	191	1141	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_003428685.1	1132028	1132028	type	True	76.8572	162	1141	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	76.8388	156	1141	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.6938	129	1141	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.6897	152	1141	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.6782	127	1141	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.6482	128	1141	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.4656	95	1141	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.3528	73	1141	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.3372	75	1141	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.1997	74	1141	95	below_threshold
Pseudomonas chlororaphis subsp. chlororaphis	strain=DSM 50083	GCA_007858335.1	333	587753	type	True	76.1254	69	1141	95	below_threshold
Pseudomonas chlororaphis subsp. chlororaphis	strain=LMG 5004	GCA_001269625.1	333	587753	type	True	76.1254	69	1141	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	75.954	88	1141	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	75.8348	77	1141	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	75.7794	63	1141	95	below_threshold
Pseudomonas poae	strain=LMG 21465	GCA_001730605.1	200451	200451	type	True	75.7369	57	1141	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	75.7134	64	1141	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	75.7109	64	1141	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.7018	52	1141	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	75.6971	75	1141	95	below_threshold
Pseudomonas poae	strain=DSM 14936	GCA_001439785.1	200451	200451	type	True	75.6965	59	1141	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:47,607] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37527/tc_result.tsv
[2023-03-19 04:11:47,607] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:47,607] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:47,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95cf4f56-29b2-401f-ae6d-1d3570d95fc8/dqc_reference/checkm_data
[2023-03-19 04:11:47,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:47,613] [INFO] Task started: CheckM
[2023-03-19 04:11:47,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37527/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37527/checkm_input OceanDNA-b37527/checkm_result
[2023-03-19 04:12:41,186] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:41,186] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:41,188] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:41,188] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:41,189] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37527/markers.fasta)
[2023-03-19 04:12:41,189] [INFO] Task started: Blastn
[2023-03-19 04:12:41,189] [INFO] Running command: blastn -query OceanDNA-b37527/markers.fasta -db /var/lib/cwl/stg95cf4f56-29b2-401f-ae6d-1d3570d95fc8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37527/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:42,453] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:42,454] [INFO] Selected 21 target genomes.
[2023-03-19 04:12:42,454] [INFO] Target genome list was writen to OceanDNA-b37527/target_genomes_gtdb.txt
[2023-03-19 04:12:42,568] [INFO] Task started: fastANI
[2023-03-19 04:12:42,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg491ed4d8-c7b3-4e74-9c7f-e951d6fe91e4/OceanDNA-b37527.fa --refList OceanDNA-b37527/target_genomes_gtdb.txt --output OceanDNA-b37527/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:57,176] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:57,188] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:12:57,188] [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_002699145.1	s__Halioglobus sp002699145	77.9466	199	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_008064665.1	s__Parahaliea maris	77.4691	186	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.3526	220	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428935.1	s__Congregibacter sp002428935	77.3428	205	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Congregibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	77.3084	190	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692965.1	s__NZNC01 sp002692965	77.2266	190	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCF_000153125.2	s__Congregibacter litoralis	77.1483	242	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Congregibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	77.1447	132	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	77.0501	195	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	76.9708	220	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764025.1	s__Pseudohaliea rubra	76.9496	191	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Pseudohaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340525.1	s__Chromatocurvus halotolerans	76.8233	157	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Chromatocurvus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_004354085.1	s__Halioglobus sp004354085	76.6897	152	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000158155.1	s__Congregibacter sp000158155	76.6525	180	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Congregibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704305.1	s__Halioglobus sp016704305	76.2321	94	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.09	98.09	0.89	0.89	2	-
GCF_013523165.1	s__Pseudomonas_E entomophila_A	76.1341	69	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	75.9367	89	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651805.1	s__Marinobacterium_A aestuarii	75.7789	63	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001439785.1	s__Pseudomonas_E poae	75.6965	59	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.09	98.80	0.95	0.92	10	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	75.6942	65	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_005780185.1	s__Halomonas urmiana	75.6802	76	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:57,188] [INFO] GTDB search result was written to OceanDNA-b37527/result_gtdb.tsv
[2023-03-19 04:12:57,189] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:57,191] [INFO] DFAST_QC result json was written to OceanDNA-b37527/dqc_result.json
[2023-03-19 04:12:57,191] [INFO] DFAST_QC completed!
[2023-03-19 04:12:57,191] [INFO] Total running time: 0h1m50s