[2023-03-15 21:48:07,258] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:07,261] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:07,261] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb6b0df1-9494-4bef-b797-f7769e8e424a/dqc_reference
[2023-03-15 21:48:08,884] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:08,884] [INFO] Task started: Prodigal
[2023-03-15 21:48:08,884] [INFO] Running command: cat /var/lib/cwl/stgbb4c7f0b-8915-4b73-a03d-1a7f19eab907/OceanDNA-b42352.fa | prodigal -d OceanDNA-b42352/cds.fna -a OceanDNA-b42352/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:12,528] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:12,529] [INFO] Task started: HMMsearch
[2023-03-15 21:48:12,529] [INFO] Running command: hmmsearch --tblout OceanDNA-b42352/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb6b0df1-9494-4bef-b797-f7769e8e424a/dqc_reference/reference_markers.hmm OceanDNA-b42352/protein.faa > /dev/null
[2023-03-15 21:48:12,685] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:12,686] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbb4c7f0b-8915-4b73-a03d-1a7f19eab907/OceanDNA-b42352.fa]
[2023-03-15 21:48:12,695] [INFO] Query marker FASTA was written to OceanDNA-b42352/markers.fasta
[2023-03-15 21:48:12,695] [INFO] Task started: Blastn
[2023-03-15 21:48:12,695] [INFO] Running command: blastn -query OceanDNA-b42352/markers.fasta -db /var/lib/cwl/stgeb6b0df1-9494-4bef-b797-f7769e8e424a/dqc_reference/reference_markers.fasta -out OceanDNA-b42352/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:14,559] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:14,559] [INFO] Selected 11 target genomes.
[2023-03-15 21:48:14,560] [INFO] Target genome list was writen to OceanDNA-b42352/target_genomes.txt
[2023-03-15 21:48:14,567] [INFO] Task started: fastANI
[2023-03-15 21:48:14,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb4c7f0b-8915-4b73-a03d-1a7f19eab907/OceanDNA-b42352.fa --refList OceanDNA-b42352/target_genomes.txt --output OceanDNA-b42352/fastani_result.tsv --threads 1
[2023-03-15 21:48:19,260] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:19,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb6b0df1-9494-4bef-b797-f7769e8e424a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:19,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb6b0df1-9494-4bef-b797-f7769e8e424a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:19,261] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:19,261] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:48:19,261] [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
--------------------------------------------------------------------------------
[2023-03-15 21:48:19,262] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42352/tc_result.tsv
[2023-03-15 21:48:19,262] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:19,262] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:19,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb6b0df1-9494-4bef-b797-f7769e8e424a/dqc_reference/checkm_data
[2023-03-15 21:48:19,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:19,270] [INFO] Task started: CheckM
[2023-03-15 21:48:19,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42352/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42352/checkm_input OceanDNA-b42352/checkm_result
[2023-03-15 21:48:34,431] [INFO] Task succeeded: CheckM
[2023-03-15 21:48:34,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:48:34,433] [INFO] ===== Completeness check finished =====
[2023-03-15 21:48:34,433] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:48:34,433] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42352/markers.fasta)
[2023-03-15 21:48:34,434] [INFO] Task started: Blastn
[2023-03-15 21:48:34,434] [INFO] Running command: blastn -query OceanDNA-b42352/markers.fasta -db /var/lib/cwl/stgeb6b0df1-9494-4bef-b797-f7769e8e424a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42352/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:35,272] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:35,273] [INFO] Selected 16 target genomes.
[2023-03-15 21:48:35,273] [INFO] Target genome list was writen to OceanDNA-b42352/target_genomes_gtdb.txt
[2023-03-15 21:48:35,308] [INFO] Task started: fastANI
[2023-03-15 21:48:35,308] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb4c7f0b-8915-4b73-a03d-1a7f19eab907/OceanDNA-b42352.fa --refList OceanDNA-b42352/target_genomes_gtdb.txt --output OceanDNA-b42352/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:48:38,424] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:38,430] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:48:38,430] [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_905478035.1	s__SCGC-AAA076-P13 sp905478035	82.7	190	218	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_000384935.1	s__SCGC-AAA076-P13 sp000384935	81.1859	166	218	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_018607365.1	s__SCGC-AAA076-P13 sp018607365	80.7905	167	218	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	77.5411	79	218	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_902591565.1	s__SCGC-AAA076-P13 sp902591565	77.415	64	218	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_902515155.1	s__SCGC-AAA076-P13 sp902515155	77.2715	60	218	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	77.1272	56	218	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_902635645.1	s__SCGC-AAA076-P13 sp902635645	77.0954	66	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.13	97.13	0.67	0.67	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:48:38,430] [INFO] GTDB search result was written to OceanDNA-b42352/result_gtdb.tsv
[2023-03-15 21:48:38,430] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:48:38,431] [INFO] DFAST_QC result json was written to OceanDNA-b42352/dqc_result.json
[2023-03-15 21:48:38,431] [INFO] DFAST_QC completed!
[2023-03-15 21:48:38,431] [INFO] Total running time: 0h0m31s