[2023-03-16 10:20:34,584] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,584] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg1751f3d1-608d-4941-8e8c-7beac51e08aa/dqc_reference
[2023-03-16 10:20:35,772] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:35,773] [INFO] Task started: Prodigal
[2023-03-16 10:20:35,773] [INFO] Running command: cat /var/lib/cwl/stgfcee8a1e-0e5a-4111-abfd-c03ea9bcf823/OceanDNA-b34942.fa | prodigal -d OceanDNA-b34942/cds.fna -a OceanDNA-b34942/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:20:44,730] [INFO] Task succeeded: Prodigal
[2023-03-16 10:20:44,730] [INFO] Task started: HMMsearch
[2023-03-16 10:20:44,731] [INFO] Running command: hmmsearch --tblout OceanDNA-b34942/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1751f3d1-608d-4941-8e8c-7beac51e08aa/dqc_reference/reference_markers.hmm OceanDNA-b34942/protein.faa > /dev/null
[2023-03-16 10:20:45,025] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:20:45,025] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfcee8a1e-0e5a-4111-abfd-c03ea9bcf823/OceanDNA-b34942.fa]
[2023-03-16 10:20:45,045] [INFO] Query marker FASTA was written to OceanDNA-b34942/markers.fasta
[2023-03-16 10:20:45,046] [INFO] Task started: Blastn
[2023-03-16 10:20:45,047] [INFO] Running command: blastn -query OceanDNA-b34942/markers.fasta -db /var/lib/cwl/stg1751f3d1-608d-4941-8e8c-7beac51e08aa/dqc_reference/reference_markers.fasta -out OceanDNA-b34942/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:45,611] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:45,612] [INFO] Selected 18 target genomes.
[2023-03-16 10:20:45,612] [INFO] Target genome list was writen to OceanDNA-b34942/target_genomes.txt
[2023-03-16 10:20:45,624] [INFO] Task started: fastANI
[2023-03-16 10:20:45,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcee8a1e-0e5a-4111-abfd-c03ea9bcf823/OceanDNA-b34942.fa --refList OceanDNA-b34942/target_genomes.txt --output OceanDNA-b34942/fastani_result.tsv --threads 1
[2023-03-16 10:20:58,847] [INFO] Task succeeded: fastANI
[2023-03-16 10:20:58,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1751f3d1-608d-4941-8e8c-7beac51e08aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:20:58,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1751f3d1-608d-4941-8e8c-7beac51e08aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:20:58,862] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:20:58,862] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:20:58,862] [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 phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	88.1405	417	478	95	below_threshold
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	88.1048	419	478	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_004103265.1	161398	161398	suspected-type	True	87.9035	408	478	95	below_threshold
Pseudoalteromonas piratica	strain=OCN003	GCA_000788395.1	1348114	1348114	type	True	78.3982	55	478	95	below_threshold
Pseudoalteromonas byunsanensis	strain=JCM 12483	GCA_001854475.1	327939	327939	type	True	77.9848	88	478	95	below_threshold
Pseudoalteromonas citrea	strain=DSM 8771	GCA_000238375.4	43655	43655	type	True	77.6504	115	478	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	77.5326	99	478	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	77.5064	88	478	95	below_threshold
Pseudoalteromonas spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	77.4779	68	478	95	below_threshold
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	77.3804	99	478	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	77.0737	71	478	95	below_threshold
Pseudoalteromonas lipolytica	strain=LMEB 39	GCA_014925285.1	570156	570156	suspected-type	True	77.0712	72	478	95	below_threshold
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	77.0587	98	478	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:20:58,862] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34942/tc_result.tsv
[2023-03-16 10:20:58,863] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:20:58,863] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:20:58,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1751f3d1-608d-4941-8e8c-7beac51e08aa/dqc_reference/checkm_data
[2023-03-16 10:20:58,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:20:58,868] [INFO] Task started: CheckM
[2023-03-16 10:20:58,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34942/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34942/checkm_input OceanDNA-b34942/checkm_result
[2023-03-16 10:21:26,428] [INFO] Task succeeded: CheckM
[2023-03-16 10:21:26,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:21:26,431] [INFO] ===== Completeness check finished =====
[2023-03-16 10:21:26,432] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:21:26,432] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34942/markers.fasta)
[2023-03-16 10:21:26,432] [INFO] Task started: Blastn
[2023-03-16 10:21:26,432] [INFO] Running command: blastn -query OceanDNA-b34942/markers.fasta -db /var/lib/cwl/stg1751f3d1-608d-4941-8e8c-7beac51e08aa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34942/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:21:27,222] [INFO] Task succeeded: Blastn
[2023-03-16 10:21:27,223] [INFO] Selected 15 target genomes.
[2023-03-16 10:21:27,223] [INFO] Target genome list was writen to OceanDNA-b34942/target_genomes_gtdb.txt
[2023-03-16 10:21:27,241] [INFO] Task started: fastANI
[2023-03-16 10:21:27,241] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcee8a1e-0e5a-4111-abfd-c03ea9bcf823/OceanDNA-b34942.fa --refList OceanDNA-b34942/target_genomes_gtdb.txt --output OceanDNA-b34942/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:21:38,518] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:38,527] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:21:38,527] [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_005886345.1	s__Pseudoalteromonas phenolica_A	89.6523	410	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.97	0.91	0.89	3	-
GCF_005876835.1	s__Pseudoalteromonas phenolica_B	89.271	429	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001444405.1	s__Pseudoalteromonas phenolica	88.1048	419	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.52	98.61	0.97	0.92	4	-
GCF_014694405.1	s__Pseudoalteromonas sp014694405	78.2655	104	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854475.1	s__Pseudoalteromonas byunsanensis	77.9848	88	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001625695.1	s__Pseudoalteromonas luteoviolacea_B	77.6475	91	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.59	99.39	0.98	0.96	4	-
GCF_001854605.1	s__Pseudoalteromonas amylolytica	77.6306	99	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009176705.1	s__Pseudoalteromonas sp009176705	77.6255	102	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001399975.1	s__Pseudoalteromonas sp001399975	77.5343	73	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550155.1	s__Pseudoalteromonas arabiensis	77.5064	88	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.77	95.60	0.91	0.90	4	-
GCF_000238255.3	s__Pseudoalteromonas spongiae	77.4779	68	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.31	96.27	0.89	0.86	4	-
GCF_900116435.1	s__Pseudoalteromonas lipolytica	77.0737	71	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.07	98.83	0.92	0.86	12	-
GCF_002723455.1	s__Pseudoalteromonas sp002723455	77.0618	76	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.50	98.50	0.93	0.93	2	-
GCF_001550135.1	s__Pseudoalteromonas shioyasakiensis	77.0587	98	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	98.58	98.56	0.94	0.92	4	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	76.9701	92	478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
--------------------------------------------------------------------------------
[2023-03-16 10:21:38,527] [INFO] GTDB search result was written to OceanDNA-b34942/result_gtdb.tsv
[2023-03-16 10:21:38,527] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:21:38,529] [INFO] DFAST_QC result json was written to OceanDNA-b34942/dqc_result.json
[2023-03-16 10:21:38,529] [INFO] DFAST_QC completed!
[2023-03-16 10:21:38,530] [INFO] Total running time: 0h1m4s