[2023-03-16 17:38:34,146] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:38:34,146] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:38:34,146] [INFO] DQC Reference Directory: /var/lib/cwl/stg15c82f22-9e11-41ee-88ee-175bab294a70/dqc_reference
[2023-03-16 17:38:35,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:38:35,422] [INFO] Task started: Prodigal
[2023-03-16 17:38:35,422] [INFO] Running command: cat /var/lib/cwl/stg1c3eefd8-9c69-4e50-b19e-fad2e29af3e6/OceanDNA-b35110.fa | prodigal -d OceanDNA-b35110/cds.fna -a OceanDNA-b35110/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:38:51,222] [INFO] Task succeeded: Prodigal
[2023-03-16 17:38:51,222] [INFO] Task started: HMMsearch
[2023-03-16 17:38:51,222] [INFO] Running command: hmmsearch --tblout OceanDNA-b35110/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15c82f22-9e11-41ee-88ee-175bab294a70/dqc_reference/reference_markers.hmm OceanDNA-b35110/protein.faa > /dev/null
[2023-03-16 17:38:51,437] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:38:51,438] [INFO] Found 6/6 markers.
[2023-03-16 17:38:51,463] [INFO] Query marker FASTA was written to OceanDNA-b35110/markers.fasta
[2023-03-16 17:38:51,464] [INFO] Task started: Blastn
[2023-03-16 17:38:51,464] [INFO] Running command: blastn -query OceanDNA-b35110/markers.fasta -db /var/lib/cwl/stg15c82f22-9e11-41ee-88ee-175bab294a70/dqc_reference/reference_markers.fasta -out OceanDNA-b35110/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:38:52,309] [INFO] Task succeeded: Blastn
[2023-03-16 17:38:52,310] [INFO] Selected 33 target genomes.
[2023-03-16 17:38:52,310] [INFO] Target genome list was writen to OceanDNA-b35110/target_genomes.txt
[2023-03-16 17:38:52,326] [INFO] Task started: fastANI
[2023-03-16 17:38:52,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c3eefd8-9c69-4e50-b19e-fad2e29af3e6/OceanDNA-b35110.fa --refList OceanDNA-b35110/target_genomes.txt --output OceanDNA-b35110/fastani_result.tsv --threads 1
[2023-03-16 17:39:12,747] [INFO] Task succeeded: fastANI
[2023-03-16 17:39:12,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15c82f22-9e11-41ee-88ee-175bab294a70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:39:12,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15c82f22-9e11-41ee-88ee-175bab294a70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:39:12,758] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:39:12,758] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:39:12,758] [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
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	78.2309	130	1002	95	below_threshold
Psychrosphaera saromensis	strain=SA4-48	GCA_002954545.1	716813	716813	type	True	78.0101	155	1002	95	below_threshold
Psychrosphaera saromensis	strain=KCTC 23240	GCA_014652155.1	716813	716813	type	True	77.9387	154	1002	95	below_threshold
Psychrosphaera aestuarii	strain=PSC101	GCA_017948405.1	1266052	1266052	type	True	77.6255	114	1002	95	below_threshold
Pseudoalteromonas piscicida	strain=ATCC 15057	GCA_000382005.1	43662	43662	type	True	77.2707	58	1002	95	below_threshold
Pseudoalteromonas piscicida	strain=JCM 20779	GCA_000238315.4	43662	43662	type	True	77.2058	56	1002	95	below_threshold
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	77.0647	77	1002	95	below_threshold
Pseudoalteromonas flavipulchra	strain=NCIMB 2033	GCA_014858715.1	137779	137779	suspected-type	True	77.0543	55	1002	95	below_threshold
Pseudoalteromonas flavipulchra	strain=LMG 20361	GCA_014596995.1	137779	137779	suspected-type	True	76.9949	53	1002	95	below_threshold
Pseudoalteromonas piratica	strain=OCN003	GCA_000788395.1	1348114	1348114	type	True	76.9822	75	1002	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	76.9524	55	1002	95	below_threshold
Marinifaba aquimaris	strain=SM1970	GCA_013328345.1	2741323	2741323	type	True	76.6297	60	1002	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	76.5577	60	1002	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	76.3915	51	1002	95	below_threshold
Pseudoalteromonas prydzensis	strain=ACAM 620	GCA_014925355.1	182141	182141	type	True	76.3754	66	1002	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	76.3034	64	1002	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	76.1872	57	1002	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:39:12,759] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35110/tc_result.tsv
[2023-03-16 17:39:12,759] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:39:12,759] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:39:12,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15c82f22-9e11-41ee-88ee-175bab294a70/dqc_reference/checkm_data
[2023-03-16 17:39:12,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:39:12,852] [INFO] Task started: CheckM
[2023-03-16 17:39:12,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35110/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35110/checkm_input OceanDNA-b35110/checkm_result
[2023-03-16 17:40:07,398] [INFO] Task succeeded: CheckM
[2023-03-16 17:40:07,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.98%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 17:40:07,405] [INFO] ===== Completeness check finished =====
[2023-03-16 17:40:07,405] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:40:07,405] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35110/markers.fasta)
[2023-03-16 17:40:07,406] [INFO] Task started: Blastn
[2023-03-16 17:40:07,406] [INFO] Running command: blastn -query OceanDNA-b35110/markers.fasta -db /var/lib/cwl/stg15c82f22-9e11-41ee-88ee-175bab294a70/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35110/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:40:08,277] [INFO] Task succeeded: Blastn
[2023-03-16 17:40:08,279] [INFO] Selected 27 target genomes.
[2023-03-16 17:40:08,280] [INFO] Target genome list was writen to OceanDNA-b35110/target_genomes_gtdb.txt
[2023-03-16 17:40:08,463] [INFO] Task started: fastANI
[2023-03-16 17:40:08,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c3eefd8-9c69-4e50-b19e-fad2e29af3e6/OceanDNA-b35110.fa --refList OceanDNA-b35110/target_genomes_gtdb.txt --output OceanDNA-b35110/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:40:35,400] [INFO] Task succeeded: fastANI
[2023-03-16 17:40:35,415] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:40:35,417] [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_017638545.1	s__Psychrosphaera sp017638545	78.2309	130	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954545.1	s__Psychrosphaera saromensis	78.0328	154	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018861025.1	s__Psychrosphaera sp018861025	77.8521	107	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009728465.1	s__Psychrosphaera haliotis	77.7227	122	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373245.1	s__Psychrosphaera sp013373245	77.6804	151	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948405.1	s__Psychrosphaera aestuarii	77.6516	113	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860345.1	s__Psychrosphaera sp018860345	77.6029	153	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238315.3	s__Pseudoalteromonas piscicida	77.2997	56	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0982	97.60	97.35	0.90	0.88	13	-
GCF_007097525.1	s__Thalassotalea_A sp007097525	77.1639	54	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696455.1	s__Pseudoalteromonas luteoviolacea_C	77.1595	53	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.80	98.80	0.96	0.96	2	-
GCF_003390335.1	s__Thalassotalea euphylliae_B	77.116	55	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016695175.1	s__Pseudoalteromonas sp002591815	77.0394	59	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6666	100.00	100.00	1.00	1.00	2	-
GCF_004103285.1	s__Pseudoalteromonas sp004103285	76.9516	52	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.27	99.27	0.97	0.97	2	-
GCF_001625695.1	s__Pseudoalteromonas luteoviolacea_B	76.7515	63	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.59	99.39	0.98	0.96	4	-
GCF_000238355.1	s__Pseudoalteromonas haloplanktis	76.4702	59	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.55	99.12	0.96	0.93	3	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	76.1659	54	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	76.1068	55	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_002276045.1	s__Pseudoalteromonas sp002276045	75.8319	51	1002	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:40:35,417] [INFO] GTDB search result was written to OceanDNA-b35110/result_gtdb.tsv
[2023-03-16 17:40:35,417] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:40:35,426] [INFO] DFAST_QC result json was written to OceanDNA-b35110/dqc_result.json
[2023-03-16 17:40:35,426] [INFO] DFAST_QC completed!
[2023-03-16 17:40:35,427] [INFO] Total running time: 0h2m1s