[2023-03-17 07:01:49,599] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2795a44-cce4-4e7b-9386-1c2d39703f51/dqc_reference
[2023-03-17 07:01:51,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:51,526] [INFO] Task started: Prodigal
[2023-03-17 07:01:51,526] [INFO] Running command: cat /var/lib/cwl/stg1d574463-7b6a-4685-8252-eff11093585c/OceanDNA-b40682.fa | prodigal -d OceanDNA-b40682/cds.fna -a OceanDNA-b40682/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:02:06,393] [INFO] Task succeeded: Prodigal
[2023-03-17 07:02:06,393] [INFO] Task started: HMMsearch
[2023-03-17 07:02:06,393] [INFO] Running command: hmmsearch --tblout OceanDNA-b40682/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2795a44-cce4-4e7b-9386-1c2d39703f51/dqc_reference/reference_markers.hmm OceanDNA-b40682/protein.faa > /dev/null
[2023-03-17 07:02:06,593] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:02:06,593] [INFO] Found 6/6 markers.
[2023-03-17 07:02:06,612] [INFO] Query marker FASTA was written to OceanDNA-b40682/markers.fasta
[2023-03-17 07:02:06,612] [INFO] Task started: Blastn
[2023-03-17 07:02:06,612] [INFO] Running command: blastn -query OceanDNA-b40682/markers.fasta -db /var/lib/cwl/stgb2795a44-cce4-4e7b-9386-1c2d39703f51/dqc_reference/reference_markers.fasta -out OceanDNA-b40682/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:07,217] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:07,218] [INFO] Selected 25 target genomes.
[2023-03-17 07:02:07,218] [INFO] Target genome list was writen to OceanDNA-b40682/target_genomes.txt
[2023-03-17 07:02:07,232] [INFO] Task started: fastANI
[2023-03-17 07:02:07,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d574463-7b6a-4685-8252-eff11093585c/OceanDNA-b40682.fa --refList OceanDNA-b40682/target_genomes.txt --output OceanDNA-b40682/fastani_result.tsv --threads 1
[2023-03-17 07:02:22,743] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:22,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2795a44-cce4-4e7b-9386-1c2d39703f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:22,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2795a44-cce4-4e7b-9386-1c2d39703f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:22,744] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:22,744] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:02:22,744] [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 07:02:22,744] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40682/tc_result.tsv
[2023-03-17 07:02:22,744] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:22,745] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:22,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2795a44-cce4-4e7b-9386-1c2d39703f51/dqc_reference/checkm_data
[2023-03-17 07:02:22,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:22,752] [INFO] Task started: CheckM
[2023-03-17 07:02:22,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40682/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40682/checkm_input OceanDNA-b40682/checkm_result
[2023-03-17 07:03:02,546] [INFO] Task succeeded: CheckM
[2023-03-17 07:03:02,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:03:02,549] [INFO] ===== Completeness check finished =====
[2023-03-17 07:03:02,549] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:03:02,549] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40682/markers.fasta)
[2023-03-17 07:03:02,549] [INFO] Task started: Blastn
[2023-03-17 07:03:02,549] [INFO] Running command: blastn -query OceanDNA-b40682/markers.fasta -db /var/lib/cwl/stgb2795a44-cce4-4e7b-9386-1c2d39703f51/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40682/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:03:03,536] [INFO] Task succeeded: Blastn
[2023-03-17 07:03:03,798] [INFO] Selected 24 target genomes.
[2023-03-17 07:03:03,798] [INFO] Target genome list was writen to OceanDNA-b40682/target_genomes_gtdb.txt
[2023-03-17 07:03:04,188] [INFO] Task started: fastANI
[2023-03-17 07:03:04,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d574463-7b6a-4685-8252-eff11093585c/OceanDNA-b40682.fa --refList OceanDNA-b40682/target_genomes_gtdb.txt --output OceanDNA-b40682/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:03:17,093] [INFO] Task succeeded: fastANI
[2023-03-17 07:03:17,098] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:03:17,098] [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_013204155.1	s__UBA9145 sp013204155	98.2613	754	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002402175.1	s__UBA9145 sp002402175	77.2136	194	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401885.1	s__UBA9145 sp002401885	77.1303	97	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730035.1	s__UBA9145 sp002730035	76.6597	69	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.69	99.69	0.91	0.91	2	-
GCA_002726595.1	s__UBA9145 sp002726595	76.5219	57	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016762975.1	s__UBA9145 sp016762975	76.434	70	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692305.1	s__UBA9145 sp009692305	76.0951	67	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:03:17,098] [INFO] GTDB search result was written to OceanDNA-b40682/result_gtdb.tsv
[2023-03-17 07:03:17,098] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:03:17,099] [INFO] DFAST_QC result json was written to OceanDNA-b40682/dqc_result.json
[2023-03-17 07:03:17,099] [INFO] DFAST_QC completed!
[2023-03-17 07:03:17,099] [INFO] Total running time: 0h1m28s