[2023-03-14 11:40:05,639] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,640] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,640] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1588fe0-8184-485d-988c-ef99a2c89d39/dqc_reference
[2023-03-14 11:40:06,755] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,756] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,756] [INFO] Running command: cat /var/lib/cwl/stgb9d0e7b9-417a-4e64-a4a7-11edeb21e55b/OceanDNA-b34982.fa | prodigal -d OceanDNA-b34982/cds.fna -a OceanDNA-b34982/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:29,009] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:29,009] [INFO] Task started: HMMsearch
[2023-03-14 11:40:29,009] [INFO] Running command: hmmsearch --tblout OceanDNA-b34982/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1588fe0-8184-485d-988c-ef99a2c89d39/dqc_reference/reference_markers.hmm OceanDNA-b34982/protein.faa > /dev/null
[2023-03-14 11:40:29,269] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:29,270] [INFO] Found 6/6 markers.
[2023-03-14 11:40:29,308] [INFO] Query marker FASTA was written to OceanDNA-b34982/markers.fasta
[2023-03-14 11:40:29,308] [INFO] Task started: Blastn
[2023-03-14 11:40:29,309] [INFO] Running command: blastn -query OceanDNA-b34982/markers.fasta -db /var/lib/cwl/stgf1588fe0-8184-485d-988c-ef99a2c89d39/dqc_reference/reference_markers.fasta -out OceanDNA-b34982/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:29,989] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:29,994] [INFO] Selected 11 target genomes.
[2023-03-14 11:40:29,994] [INFO] Target genome list was writen to OceanDNA-b34982/target_genomes.txt
[2023-03-14 11:40:30,001] [INFO] Task started: fastANI
[2023-03-14 11:40:30,001] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9d0e7b9-417a-4e64-a4a7-11edeb21e55b/OceanDNA-b34982.fa --refList OceanDNA-b34982/target_genomes.txt --output OceanDNA-b34982/fastani_result.tsv --threads 1
[2023-03-14 11:40:41,179] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:41,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1588fe0-8184-485d-988c-ef99a2c89d39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:40:41,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1588fe0-8184-485d-988c-ef99a2c89d39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:40:41,186] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 11:40:41,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 11:40:41,186] [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 arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	99.0472	1294	1375	95	conclusive
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	86.6599	1022	1375	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	86.5748	1011	1375	95	below_threshold
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	86.5374	1015	1375	95	below_threshold
Pseudoalteromonas lipolytica	strain=LMEB 39	GCA_014925285.1	570156	570156	suspected-type	True	83.2617	938	1375	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	83.2616	933	1375	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	79.5452	444	1375	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	76.5587	57	1375	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	76.5568	57	1375	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:40:41,188] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34982/tc_result.tsv
[2023-03-14 11:40:41,190] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:40:41,191] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:40:41,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1588fe0-8184-485d-988c-ef99a2c89d39/dqc_reference/checkm_data
[2023-03-14 11:40:41,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:40:41,200] [INFO] Task started: CheckM
[2023-03-14 11:40:41,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34982/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34982/checkm_input OceanDNA-b34982/checkm_result
[2023-03-14 11:41:36,659] [INFO] Task succeeded: CheckM
[2023-03-14 11:41:36,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:41:36,677] [INFO] ===== Completeness check finished =====
[2023-03-14 11:41:36,677] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:41:36,678] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34982/markers.fasta)
[2023-03-14 11:41:36,679] [INFO] Task started: Blastn
[2023-03-14 11:41:36,679] [INFO] Running command: blastn -query OceanDNA-b34982/markers.fasta -db /var/lib/cwl/stgf1588fe0-8184-485d-988c-ef99a2c89d39/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34982/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:41:37,736] [INFO] Task succeeded: Blastn
[2023-03-14 11:41:37,741] [INFO] Selected 11 target genomes.
[2023-03-14 11:41:37,741] [INFO] Target genome list was writen to OceanDNA-b34982/target_genomes_gtdb.txt
[2023-03-14 11:41:37,774] [INFO] Task started: fastANI
[2023-03-14 11:41:37,774] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9d0e7b9-417a-4e64-a4a7-11edeb21e55b/OceanDNA-b34982.fa --refList OceanDNA-b34982/target_genomes_gtdb.txt --output OceanDNA-b34982/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:41:47,677] [INFO] Task succeeded: fastANI
[2023-03-14 11:41:47,684] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:41:47,684] [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_001550155.1	s__Pseudoalteromonas arabiensis	99.0472	1294	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.77	95.60	0.91	0.90	4	conclusive
GCA_002684115.1	s__Pseudoalteromonas sp002684115	88.1003	212	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	97.90	97.71	0.79	0.79	5	-
GCF_001550135.1	s__Pseudoalteromonas shioyasakiensis	86.6697	1021	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	98.58	98.56	0.94	0.92	4	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	86.5748	1011	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_001469895.1	s__Pseudoalteromonas sp001469895	86.5708	973	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.7314	N/A	N/A	N/A	N/A	1	-
GCF_019134595.1	s__Pseudoalteromonas shioyasakiensis_A	86.4413	1000	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6918	N/A	N/A	N/A	N/A	1	-
GCF_013391845.1	s__Pseudoalteromonas sp002685175	86.4248	840	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.05	98.96	0.91	0.83	5	-
GCF_013349995.1	s__Pseudoalteromonas sp013349995	86.3857	972	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.6093	97.46	97.37	0.85	0.84	6	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	86.2689	983	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_004792295.1	s__Pseudoalteromonas lipolytica_C	85.7936	994	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.42	98.24	0.87	0.68	9	-
GCF_900116435.1	s__Pseudoalteromonas lipolytica	83.2737	932	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.07	98.83	0.92	0.86	12	-
--------------------------------------------------------------------------------
[2023-03-14 11:41:47,687] [INFO] GTDB search result was written to OceanDNA-b34982/result_gtdb.tsv
[2023-03-14 11:41:47,688] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:41:47,692] [INFO] DFAST_QC result json was written to OceanDNA-b34982/dqc_result.json
[2023-03-14 11:41:47,692] [INFO] DFAST_QC completed!
[2023-03-14 11:41:47,692] [INFO] Total running time: 0h1m42s