[2023-03-17 04:35:35,517] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:35:35,517] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:35:35,517] [INFO] DQC Reference Directory: /var/lib/cwl/stge8ffb4c8-e4f8-4141-bbf2-660a5a30f7c9/dqc_reference
[2023-03-17 04:35:36,687] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:35:36,687] [INFO] Task started: Prodigal
[2023-03-17 04:35:36,688] [INFO] Running command: cat /var/lib/cwl/stg396151b9-f344-4ddd-9422-ec4a02975ee0/OceanDNA-b42287.fa | prodigal -d OceanDNA-b42287/cds.fna -a OceanDNA-b42287/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:35:39,132] [INFO] Task succeeded: Prodigal
[2023-03-17 04:35:39,133] [INFO] Task started: HMMsearch
[2023-03-17 04:35:39,133] [INFO] Running command: hmmsearch --tblout OceanDNA-b42287/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8ffb4c8-e4f8-4141-bbf2-660a5a30f7c9/dqc_reference/reference_markers.hmm OceanDNA-b42287/protein.faa > /dev/null
[2023-03-17 04:35:39,311] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:35:39,312] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg396151b9-f344-4ddd-9422-ec4a02975ee0/OceanDNA-b42287.fa]
[2023-03-17 04:35:39,319] [INFO] Query marker FASTA was written to OceanDNA-b42287/markers.fasta
[2023-03-17 04:35:39,325] [INFO] Task started: Blastn
[2023-03-17 04:35:39,325] [INFO] Running command: blastn -query OceanDNA-b42287/markers.fasta -db /var/lib/cwl/stge8ffb4c8-e4f8-4141-bbf2-660a5a30f7c9/dqc_reference/reference_markers.fasta -out OceanDNA-b42287/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:35:40,037] [INFO] Task succeeded: Blastn
[2023-03-17 04:35:40,037] [INFO] Selected 13 target genomes.
[2023-03-17 04:35:40,038] [INFO] Target genome list was writen to OceanDNA-b42287/target_genomes.txt
[2023-03-17 04:35:40,045] [INFO] Task started: fastANI
[2023-03-17 04:35:40,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg396151b9-f344-4ddd-9422-ec4a02975ee0/OceanDNA-b42287.fa --refList OceanDNA-b42287/target_genomes.txt --output OceanDNA-b42287/fastani_result.tsv --threads 1
[2023-03-17 04:35:46,380] [INFO] Task succeeded: fastANI
[2023-03-17 04:35:46,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8ffb4c8-e4f8-4141-bbf2-660a5a30f7c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:35:46,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8ffb4c8-e4f8-4141-bbf2-660a5a30f7c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:35:46,381] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:35:46,381] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:35:46,381] [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
--------------------------------------------------------------------------------
[2023-03-17 04:35:46,381] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42287/tc_result.tsv
[2023-03-17 04:35:46,381] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:35:46,381] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:35:46,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8ffb4c8-e4f8-4141-bbf2-660a5a30f7c9/dqc_reference/checkm_data
[2023-03-17 04:35:46,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:35:46,386] [INFO] Task started: CheckM
[2023-03-17 04:35:46,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42287/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42287/checkm_input OceanDNA-b42287/checkm_result
[2023-03-17 04:36:04,312] [INFO] Task succeeded: CheckM
[2023-03-17 04:36:04,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:36:04,313] [INFO] ===== Completeness check finished =====
[2023-03-17 04:36:04,314] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:36:04,314] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42287/markers.fasta)
[2023-03-17 04:36:04,315] [INFO] Task started: Blastn
[2023-03-17 04:36:04,316] [INFO] Running command: blastn -query OceanDNA-b42287/markers.fasta -db /var/lib/cwl/stge8ffb4c8-e4f8-4141-bbf2-660a5a30f7c9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42287/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:36:05,636] [INFO] Task succeeded: Blastn
[2023-03-17 04:36:05,637] [INFO] Selected 13 target genomes.
[2023-03-17 04:36:05,637] [INFO] Target genome list was writen to OceanDNA-b42287/target_genomes_gtdb.txt
[2023-03-17 04:36:06,020] [INFO] Task started: fastANI
[2023-03-17 04:36:06,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg396151b9-f344-4ddd-9422-ec4a02975ee0/OceanDNA-b42287.fa --refList OceanDNA-b42287/target_genomes_gtdb.txt --output OceanDNA-b42287/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:36:08,300] [INFO] Task succeeded: fastANI
[2023-03-17 04:36:08,308] [INFO] Found 13 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-17 04:36:08,308] [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_902560315.1	s__SAR86A sp902560315	96.3196	121	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.47	95.47	0.82	0.82	2	inconclusive
GCA_902517505.1	s__SAR86A sp902517505	95.4697	121	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.73	97.59	0.82	0.80	3	inconclusive
GCA_902556105.1	s__SAR86A sp902556105	79.7591	65	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902612915.1	s__SAR86A sp902612915	79.5844	85	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.80	95.61	0.84	0.75	10	-
GCA_902631785.1	s__SAR86A sp902631785	79.5614	76	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
GCA_902541175.1	s__SAR86A sp902541175	79.302	90	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.65	95.31	0.89	0.85	3	-
GCA_902617045.1	s__SAR86A sp902617045	79.0358	95	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902586925.1	s__SAR86A sp902586925	78.9451	79	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.82	96.82	0.89	0.89	2	-
GCA_902591925.1	s__SAR86A sp902591925	78.8947	95	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_902583575.1	s__SAR86A sp902583575	78.5214	79	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520725.1	s__SAR86A sp902520725	78.4622	68	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.82	99.82	0.73	0.73	2	-
GCA_902551185.1	s__SAR86A sp902551185	78.3494	62	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.17	99.17	0.78	0.78	2	-
GCA_902517425.1	s__SAR86A sp902517425	78.299	64	140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:36:08,308] [INFO] GTDB search result was written to OceanDNA-b42287/result_gtdb.tsv
[2023-03-17 04:36:08,308] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:36:08,309] [INFO] DFAST_QC result json was written to OceanDNA-b42287/dqc_result.json
[2023-03-17 04:36:08,309] [INFO] DFAST_QC completed!
[2023-03-17 04:36:08,309] [INFO] Total running time: 0h0m33s