[2023-03-16 16:53:43,517] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:53:43,517] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:53:43,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f5bc1f0-98fc-49b2-93a6-f89a287c012b/dqc_reference
[2023-03-16 16:53:44,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:53:44,607] [INFO] Task started: Prodigal
[2023-03-16 16:53:44,607] [INFO] Running command: cat /var/lib/cwl/stg2714b064-fa08-40a7-a0fb-31ac68860300/OceanDNA-b41321.fa | prodigal -d OceanDNA-b41321/cds.fna -a OceanDNA-b41321/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:53:57,105] [INFO] Task succeeded: Prodigal
[2023-03-16 16:53:57,105] [INFO] Task started: HMMsearch
[2023-03-16 16:53:57,105] [INFO] Running command: hmmsearch --tblout OceanDNA-b41321/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f5bc1f0-98fc-49b2-93a6-f89a287c012b/dqc_reference/reference_markers.hmm OceanDNA-b41321/protein.faa > /dev/null
[2023-03-16 16:53:57,298] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:53:57,299] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2714b064-fa08-40a7-a0fb-31ac68860300/OceanDNA-b41321.fa]
[2023-03-16 16:53:57,319] [INFO] Query marker FASTA was written to OceanDNA-b41321/markers.fasta
[2023-03-16 16:53:57,319] [INFO] Task started: Blastn
[2023-03-16 16:53:57,319] [INFO] Running command: blastn -query OceanDNA-b41321/markers.fasta -db /var/lib/cwl/stg5f5bc1f0-98fc-49b2-93a6-f89a287c012b/dqc_reference/reference_markers.fasta -out OceanDNA-b41321/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:53:57,937] [INFO] Task succeeded: Blastn
[2023-03-16 16:53:57,938] [INFO] Selected 26 target genomes.
[2023-03-16 16:53:57,938] [INFO] Target genome list was writen to OceanDNA-b41321/target_genomes.txt
[2023-03-16 16:53:57,950] [INFO] Task started: fastANI
[2023-03-16 16:53:57,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg2714b064-fa08-40a7-a0fb-31ac68860300/OceanDNA-b41321.fa --refList OceanDNA-b41321/target_genomes.txt --output OceanDNA-b41321/fastani_result.tsv --threads 1
[2023-03-16 16:54:11,894] [INFO] Task succeeded: fastANI
[2023-03-16 16:54:11,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f5bc1f0-98fc-49b2-93a6-f89a287c012b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:54:11,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f5bc1f0-98fc-49b2-93a6-f89a287c012b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:54:11,898] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:54:11,898] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:54:11,898] [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
Bermanella marisrubri	strain=RED65	GCA_012295615.1	207949	207949	type	True	77.6085	99	730	95	below_threshold
Bermanella marisrubri	strain=RED65	GCA_000153565.1	207949	207949	type	True	77.5785	102	730	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:54:11,899] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41321/tc_result.tsv
[2023-03-16 16:54:11,899] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:54:11,899] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:54:11,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f5bc1f0-98fc-49b2-93a6-f89a287c012b/dqc_reference/checkm_data
[2023-03-16 16:54:11,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:54:11,918] [INFO] Task started: CheckM
[2023-03-16 16:54:11,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41321/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41321/checkm_input OceanDNA-b41321/checkm_result
[2023-03-16 16:55:00,095] [INFO] Task succeeded: CheckM
[2023-03-16 16:55:00,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:55:00,098] [INFO] ===== Completeness check finished =====
[2023-03-16 16:55:00,098] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:55:00,098] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41321/markers.fasta)
[2023-03-16 16:55:00,099] [INFO] Task started: Blastn
[2023-03-16 16:55:00,099] [INFO] Running command: blastn -query OceanDNA-b41321/markers.fasta -db /var/lib/cwl/stg5f5bc1f0-98fc-49b2-93a6-f89a287c012b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41321/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:55:01,098] [INFO] Task succeeded: Blastn
[2023-03-16 16:55:01,099] [INFO] Selected 24 target genomes.
[2023-03-16 16:55:01,099] [INFO] Target genome list was writen to OceanDNA-b41321/target_genomes_gtdb.txt
[2023-03-16 16:55:01,115] [INFO] Task started: fastANI
[2023-03-16 16:55:01,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg2714b064-fa08-40a7-a0fb-31ac68860300/OceanDNA-b41321.fa --refList OceanDNA-b41321/target_genomes_gtdb.txt --output OceanDNA-b41321/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:55:26,749] [INFO] Task succeeded: fastANI
[2023-03-16 16:55:26,753] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:55:26,753] [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_002683575.1	s__Bermanella sp002683575	78.1264	166	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	99.58	99.58	0.89	0.89	2	-
GCA_013373125.1	s__Bermanella sp013373125	77.9812	181	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012295615.1	s__Bermanella marisrubri	77.6085	99	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002162985.1	s__Bermanella sp002162985	77.3746	83	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:55:26,753] [INFO] GTDB search result was written to OceanDNA-b41321/result_gtdb.tsv
[2023-03-16 16:55:26,754] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:55:26,755] [INFO] DFAST_QC result json was written to OceanDNA-b41321/dqc_result.json
[2023-03-16 16:55:26,755] [INFO] DFAST_QC completed!
[2023-03-16 16:55:26,755] [INFO] Total running time: 0h1m43s