[2023-03-18 23:44:06,379] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,379] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg62f2def5-dc38-44b3-8cd1-9f76af0f9378/dqc_reference
[2023-03-18 23:44:07,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,497] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,498] [INFO] Running command: cat /var/lib/cwl/stg3056437c-e083-45fd-962a-42732f7d78fd/OceanDNA-b42319.fa | prodigal -d OceanDNA-b42319/cds.fna -a OceanDNA-b42319/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:12,110] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:12,110] [INFO] Task started: HMMsearch
[2023-03-18 23:44:12,110] [INFO] Running command: hmmsearch --tblout OceanDNA-b42319/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62f2def5-dc38-44b3-8cd1-9f76af0f9378/dqc_reference/reference_markers.hmm OceanDNA-b42319/protein.faa > /dev/null
[2023-03-18 23:44:12,264] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:12,265] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3056437c-e083-45fd-962a-42732f7d78fd/OceanDNA-b42319.fa]
[2023-03-18 23:44:12,273] [INFO] Query marker FASTA was written to OceanDNA-b42319/markers.fasta
[2023-03-18 23:44:12,274] [INFO] Task started: Blastn
[2023-03-18 23:44:12,274] [INFO] Running command: blastn -query OceanDNA-b42319/markers.fasta -db /var/lib/cwl/stg62f2def5-dc38-44b3-8cd1-9f76af0f9378/dqc_reference/reference_markers.fasta -out OceanDNA-b42319/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:12,766] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:12,766] [INFO] Selected 12 target genomes.
[2023-03-18 23:44:12,766] [INFO] Target genome list was writen to OceanDNA-b42319/target_genomes.txt
[2023-03-18 23:44:12,775] [INFO] Task started: fastANI
[2023-03-18 23:44:12,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg3056437c-e083-45fd-962a-42732f7d78fd/OceanDNA-b42319.fa --refList OceanDNA-b42319/target_genomes.txt --output OceanDNA-b42319/fastani_result.tsv --threads 1
[2023-03-18 23:44:18,092] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:18,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62f2def5-dc38-44b3-8cd1-9f76af0f9378/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:18,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62f2def5-dc38-44b3-8cd1-9f76af0f9378/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:18,093] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:18,093] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:44:18,093] [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
--------------------------------------------------------------------------------
[2023-03-18 23:44:18,093] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42319/tc_result.tsv
[2023-03-18 23:44:18,093] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:18,093] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:18,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62f2def5-dc38-44b3-8cd1-9f76af0f9378/dqc_reference/checkm_data
[2023-03-18 23:44:18,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:18,172] [INFO] Task started: CheckM
[2023-03-18 23:44:18,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42319/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42319/checkm_input OceanDNA-b42319/checkm_result
[2023-03-18 23:44:35,952] [INFO] Task succeeded: CheckM
[2023-03-18 23:44:35,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:44:35,954] [INFO] ===== Completeness check finished =====
[2023-03-18 23:44:35,954] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:44:35,954] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42319/markers.fasta)
[2023-03-18 23:44:35,955] [INFO] Task started: Blastn
[2023-03-18 23:44:35,955] [INFO] Running command: blastn -query OceanDNA-b42319/markers.fasta -db /var/lib/cwl/stg62f2def5-dc38-44b3-8cd1-9f76af0f9378/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42319/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:36,620] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:36,621] [INFO] Selected 14 target genomes.
[2023-03-18 23:44:36,621] [INFO] Target genome list was writen to OceanDNA-b42319/target_genomes_gtdb.txt
[2023-03-18 23:44:36,630] [INFO] Task started: fastANI
[2023-03-18 23:44:36,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg3056437c-e083-45fd-962a-42732f7d78fd/OceanDNA-b42319.fa --refList OceanDNA-b42319/target_genomes_gtdb.txt --output OceanDNA-b42319/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:44:39,545] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:39,552] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:44:39,553] [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_018607365.1	s__SCGC-AAA076-P13 sp018607365	98.732	270	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000384935.1	s__SCGC-AAA076-P13 sp000384935	94.6117	265	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478035.1	s__SCGC-AAA076-P13 sp905478035	81.3907	247	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000385055.1	s__SCGC-AAA076-P13 sp000385055	78.1579	112	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.19	98.19	0.89	0.89	2	-
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	77.7775	107	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.77	97.77	0.94	0.94	2	-
GCA_902591565.1	s__SCGC-AAA076-P13 sp902591565	77.7195	85	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591665.1	s__SCGC-AAA076-P13 sp902591665	77.6003	94	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	99.81	99.81	0.85	0.85	2	-
GCA_902557705.1	s__SCGC-AAA076-P13 sp902557705	77.4933	76	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024215.1	s__SCGC-AAA076-P13 sp010024215	77.35	67	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.04	96.58	0.74	0.68	5	-
GCA_902515155.1	s__SCGC-AAA076-P13 sp902515155	77.2449	94	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558375.1	s__SCGC-AAA076-P13 sp902558375	77.0656	77	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331505.1	s__MED-G85 sp003331505	76.7389	54	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G85	95.0	98.80	96.15	0.89	0.83	6	-
--------------------------------------------------------------------------------
[2023-03-18 23:44:39,553] [INFO] GTDB search result was written to OceanDNA-b42319/result_gtdb.tsv
[2023-03-18 23:44:39,553] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:44:39,554] [INFO] DFAST_QC result json was written to OceanDNA-b42319/dqc_result.json
[2023-03-18 23:44:39,554] [INFO] DFAST_QC completed!
[2023-03-18 23:44:39,554] [INFO] Total running time: 0h0m33s