[2023-03-15 17:09:05,940] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:09:05,941] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:09:05,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg88d0b403-243c-4a96-a7de-10ac5107dbbc/dqc_reference
[2023-03-15 17:09:07,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:09:07,761] [INFO] Task started: Prodigal
[2023-03-15 17:09:07,762] [INFO] Running command: cat /var/lib/cwl/stga7792f5d-a933-462d-8dea-5529e43db439/OceanDNA-b26761.fa | prodigal -d OceanDNA-b26761/cds.fna -a OceanDNA-b26761/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:09:27,384] [INFO] Task succeeded: Prodigal
[2023-03-15 17:09:27,384] [INFO] Task started: HMMsearch
[2023-03-15 17:09:27,384] [INFO] Running command: hmmsearch --tblout OceanDNA-b26761/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88d0b403-243c-4a96-a7de-10ac5107dbbc/dqc_reference/reference_markers.hmm OceanDNA-b26761/protein.faa > /dev/null
[2023-03-15 17:09:27,602] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:09:27,603] [INFO] Found 6/6 markers.
[2023-03-15 17:09:27,625] [INFO] Query marker FASTA was written to OceanDNA-b26761/markers.fasta
[2023-03-15 17:09:27,628] [INFO] Task started: Blastn
[2023-03-15 17:09:27,628] [INFO] Running command: blastn -query OceanDNA-b26761/markers.fasta -db /var/lib/cwl/stg88d0b403-243c-4a96-a7de-10ac5107dbbc/dqc_reference/reference_markers.fasta -out OceanDNA-b26761/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:09:28,219] [INFO] Task succeeded: Blastn
[2023-03-15 17:09:28,222] [INFO] Selected 32 target genomes.
[2023-03-15 17:09:28,223] [INFO] Target genome list was writen to OceanDNA-b26761/target_genomes.txt
[2023-03-15 17:09:28,242] [INFO] Task started: fastANI
[2023-03-15 17:09:28,243] [INFO] Running command: fastANI --query /var/lib/cwl/stga7792f5d-a933-462d-8dea-5529e43db439/OceanDNA-b26761.fa --refList OceanDNA-b26761/target_genomes.txt --output OceanDNA-b26761/fastani_result.tsv --threads 1
[2023-03-15 17:09:50,954] [INFO] Task succeeded: fastANI
[2023-03-15 17:09:50,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88d0b403-243c-4a96-a7de-10ac5107dbbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:09:50,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88d0b403-243c-4a96-a7de-10ac5107dbbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:09:50,955] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:09:50,955] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:09:50,955] [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 17:09:50,960] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26761/tc_result.tsv
[2023-03-15 17:09:50,964] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:09:50,964] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:09:50,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88d0b403-243c-4a96-a7de-10ac5107dbbc/dqc_reference/checkm_data
[2023-03-15 17:09:50,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:09:50,975] [INFO] Task started: CheckM
[2023-03-15 17:09:50,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26761/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26761/checkm_input OceanDNA-b26761/checkm_result
[2023-03-15 17:10:41,170] [INFO] Task succeeded: CheckM
[2023-03-15 17:10:41,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:10:41,202] [INFO] ===== Completeness check finished =====
[2023-03-15 17:10:41,202] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:10:41,202] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26761/markers.fasta)
[2023-03-15 17:10:41,203] [INFO] Task started: Blastn
[2023-03-15 17:10:41,203] [INFO] Running command: blastn -query OceanDNA-b26761/markers.fasta -db /var/lib/cwl/stg88d0b403-243c-4a96-a7de-10ac5107dbbc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26761/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:10:42,392] [INFO] Task succeeded: Blastn
[2023-03-15 17:10:42,402] [INFO] Selected 12 target genomes.
[2023-03-15 17:10:42,402] [INFO] Target genome list was writen to OceanDNA-b26761/target_genomes_gtdb.txt
[2023-03-15 17:10:42,434] [INFO] Task started: fastANI
[2023-03-15 17:10:42,434] [INFO] Running command: fastANI --query /var/lib/cwl/stga7792f5d-a933-462d-8dea-5529e43db439/OceanDNA-b26761.fa --refList OceanDNA-b26761/target_genomes_gtdb.txt --output OceanDNA-b26761/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:10:50,158] [INFO] Task succeeded: fastANI
[2023-03-15 17:10:50,163] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:10:50,163] [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_013214705.1	s__OCS116 sp013214705	99.9978	1058	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__OSC116;g__OCS116	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002402005.2	s__OCS116 sp002402005	78.9479	267	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__OSC116;g__OCS116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400495.2	s__OCS116 sp002400495	78.5357	365	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__OSC116;g__OCS116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401855.1	s__OCS116 sp002401855	78.3988	342	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__OSC116;g__OCS116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744975.1	s__OCS116 sp016744975	77.5587	191	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__OSC116;g__OCS116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214985.1	s__OCS116 sp013214985	77.3874	157	1068	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__OSC116;g__OCS116	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:10:50,165] [INFO] GTDB search result was written to OceanDNA-b26761/result_gtdb.tsv
[2023-03-15 17:10:50,166] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:10:50,170] [INFO] DFAST_QC result json was written to OceanDNA-b26761/dqc_result.json
[2023-03-15 17:10:50,170] [INFO] DFAST_QC completed!
[2023-03-15 17:10:50,170] [INFO] Total running time: 0h1m44s