[2023-03-18 10:24:55,273] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:24:55,274] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:24:55,274] [INFO] DQC Reference Directory: /var/lib/cwl/stg23069bb5-055e-4df1-9918-5e2da7f8b48a/dqc_reference
[2023-03-18 10:24:56,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:24:56,377] [INFO] Task started: Prodigal
[2023-03-18 10:24:56,378] [INFO] Running command: cat /var/lib/cwl/stg46d492e4-54e4-44d7-8a86-44660ff963ca/OceanDNA-b34940.fa | prodigal -d OceanDNA-b34940/cds.fna -a OceanDNA-b34940/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:25:13,290] [INFO] Task succeeded: Prodigal
[2023-03-18 10:25:13,290] [INFO] Task started: HMMsearch
[2023-03-18 10:25:13,290] [INFO] Running command: hmmsearch --tblout OceanDNA-b34940/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23069bb5-055e-4df1-9918-5e2da7f8b48a/dqc_reference/reference_markers.hmm OceanDNA-b34940/protein.faa > /dev/null
[2023-03-18 10:25:13,526] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:25:13,527] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg46d492e4-54e4-44d7-8a86-44660ff963ca/OceanDNA-b34940.fa]
[2023-03-18 10:25:13,561] [INFO] Query marker FASTA was written to OceanDNA-b34940/markers.fasta
[2023-03-18 10:25:13,561] [INFO] Task started: Blastn
[2023-03-18 10:25:13,561] [INFO] Running command: blastn -query OceanDNA-b34940/markers.fasta -db /var/lib/cwl/stg23069bb5-055e-4df1-9918-5e2da7f8b48a/dqc_reference/reference_markers.fasta -out OceanDNA-b34940/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:25:14,157] [INFO] Task succeeded: Blastn
[2023-03-18 10:25:14,161] [INFO] Selected 21 target genomes.
[2023-03-18 10:25:14,161] [INFO] Target genome list was writen to OceanDNA-b34940/target_genomes.txt
[2023-03-18 10:25:14,174] [INFO] Task started: fastANI
[2023-03-18 10:25:14,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg46d492e4-54e4-44d7-8a86-44660ff963ca/OceanDNA-b34940.fa --refList OceanDNA-b34940/target_genomes.txt --output OceanDNA-b34940/fastani_result.tsv --threads 1
[2023-03-18 10:25:28,648] [INFO] Task succeeded: fastANI
[2023-03-18 10:25:28,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23069bb5-055e-4df1-9918-5e2da7f8b48a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:25:28,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23069bb5-055e-4df1-9918-5e2da7f8b48a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:25:28,658] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:25:28,659] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:25:28,659] [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
Pseudoalteromonas piratica	strain=OCN003	GCA_000788395.1	1348114	1348114	type	True	80.2522	439	1063	95	below_threshold
Pseudoalteromonas spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	79.9449	446	1063	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	77.7488	140	1063	95	below_threshold
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	77.7486	138	1063	95	below_threshold
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	77.6131	130	1063	95	below_threshold
Pseudoalteromonas citrea	strain=DSM 8771	GCA_000238375.4	43655	43655	type	True	77.5843	101	1063	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	77.4684	115	1063	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	77.4172	131	1063	95	below_threshold
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	77.3395	132	1063	95	below_threshold
Pseudoalteromonas flavipulchra	strain=LMG 20361	GCA_014596995.1	137779	137779	suspected-type	True	77.217	96	1063	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	77.1516	104	1063	95	below_threshold
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	77.0795	104	1063	95	below_threshold
Pseudoalteromonas ulvae	strain=UL12	GCA_014925405.1	107327	107327	type	True	77.0272	118	1063	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	76.9752	100	1063	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	76.9731	99	1063	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	76.9096	116	1063	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:25:28,661] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34940/tc_result.tsv
[2023-03-18 10:25:28,664] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:25:28,664] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:25:28,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23069bb5-055e-4df1-9918-5e2da7f8b48a/dqc_reference/checkm_data
[2023-03-18 10:25:28,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:25:28,672] [INFO] Task started: CheckM
[2023-03-18 10:25:28,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34940/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34940/checkm_input OceanDNA-b34940/checkm_result
[2023-03-18 10:26:13,513] [INFO] Task succeeded: CheckM
[2023-03-18 10:26:13,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.33%
Contamintation: 5.01%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 10:26:13,567] [INFO] ===== Completeness check finished =====
[2023-03-18 10:26:13,567] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:26:13,567] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34940/markers.fasta)
[2023-03-18 10:26:13,569] [INFO] Task started: Blastn
[2023-03-18 10:26:13,569] [INFO] Running command: blastn -query OceanDNA-b34940/markers.fasta -db /var/lib/cwl/stg23069bb5-055e-4df1-9918-5e2da7f8b48a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34940/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:26:14,529] [INFO] Task succeeded: Blastn
[2023-03-18 10:26:14,533] [INFO] Selected 22 target genomes.
[2023-03-18 10:26:14,533] [INFO] Target genome list was writen to OceanDNA-b34940/target_genomes_gtdb.txt
[2023-03-18 10:26:14,764] [INFO] Task started: fastANI
[2023-03-18 10:26:14,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg46d492e4-54e4-44d7-8a86-44660ff963ca/OceanDNA-b34940.fa --refList OceanDNA-b34940/target_genomes_gtdb.txt --output OceanDNA-b34940/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:26:30,402] [INFO] Task succeeded: fastANI
[2023-03-18 10:26:30,414] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:26:30,414] [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_000788395.1	s__Pseudoalteromonas piratica	80.2522	439	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238255.3	s__Pseudoalteromonas spongiae	79.9566	445	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.31	96.27	0.89	0.86	4	-
GCF_001399975.1	s__Pseudoalteromonas sp001399975	79.8253	444	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019134595.1	s__Pseudoalteromonas shioyasakiensis_A	77.7623	124	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6918	N/A	N/A	N/A	N/A	1	-
GCF_001444405.1	s__Pseudoalteromonas phenolica	77.7486	138	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.52	98.61	0.97	0.92	4	-
GCF_002744175.1	s__Pseudoalteromonas piscicida_B	77.6065	90	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005886535.1	s__Pseudoalteromonas sp005886535	77.606	86	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469895.1	s__Pseudoalteromonas sp001469895	77.5856	133	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.7314	N/A	N/A	N/A	N/A	1	-
GCF_000238375.3	s__Pseudoalteromonas citrea	77.5843	101	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001625575.1	s__Pseudoalteromonas luteoviolacea_E	77.4526	87	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.25	97.25	0.92	0.92	2	-
GCF_013349995.1	s__Pseudoalteromonas sp013349995	77.4464	133	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.6093	97.46	97.37	0.85	0.84	6	-
GCF_004792295.1	s__Pseudoalteromonas lipolytica_C	77.3935	127	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.42	98.24	0.87	0.68	9	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	77.3001	142	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_002723455.1	s__Pseudoalteromonas sp002723455	77.2316	92	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.50	98.50	0.93	0.93	2	-
GCF_001653135.1	s__Pseudoalteromonas neustonica	77.1648	90	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.11	98.62	0.93	0.89	5	-
GCA_007988745.1	s__Pseudoalteromonas atlantica	77.1422	98	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	-
GCF_001469215.1	s__Pseudoalteromonas sp001469215	77.1274	103	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002165575.1	s__Pseudoalteromonas sp002165575	77.0968	117	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	77.0119	99	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_001625695.1	s__Pseudoalteromonas luteoviolacea_B	76.9833	102	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.59	99.39	0.98	0.96	4	-
GCF_000238275.3	s__Pseudoalteromonas undina	76.9096	116	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
--------------------------------------------------------------------------------
[2023-03-18 10:26:30,416] [INFO] GTDB search result was written to OceanDNA-b34940/result_gtdb.tsv
[2023-03-18 10:26:30,420] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:26:30,424] [INFO] DFAST_QC result json was written to OceanDNA-b34940/dqc_result.json
[2023-03-18 10:26:30,425] [INFO] DFAST_QC completed!
[2023-03-18 10:26:30,425] [INFO] Total running time: 0h1m35s