[2023-03-17 09:14:28,744] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:14:28,744] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:14:28,744] [INFO] DQC Reference Directory: /var/lib/cwl/stga1282cb7-3b72-46a7-9445-f3b2610c72ff/dqc_reference
[2023-03-17 09:14:29,853] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:14:29,854] [INFO] Task started: Prodigal
[2023-03-17 09:14:29,854] [INFO] Running command: cat /var/lib/cwl/stge087f9f9-a840-4f96-a41c-61df311dee85/OceanDNA-b35376.fa | prodigal -d OceanDNA-b35376/cds.fna -a OceanDNA-b35376/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:14:50,214] [INFO] Task succeeded: Prodigal
[2023-03-17 09:14:50,215] [INFO] Task started: HMMsearch
[2023-03-17 09:14:50,215] [INFO] Running command: hmmsearch --tblout OceanDNA-b35376/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1282cb7-3b72-46a7-9445-f3b2610c72ff/dqc_reference/reference_markers.hmm OceanDNA-b35376/protein.faa > /dev/null
[2023-03-17 09:14:50,434] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:14:50,434] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge087f9f9-a840-4f96-a41c-61df311dee85/OceanDNA-b35376.fa]
[2023-03-17 09:14:50,461] [INFO] Query marker FASTA was written to OceanDNA-b35376/markers.fasta
[2023-03-17 09:14:50,462] [INFO] Task started: Blastn
[2023-03-17 09:14:50,462] [INFO] Running command: blastn -query OceanDNA-b35376/markers.fasta -db /var/lib/cwl/stga1282cb7-3b72-46a7-9445-f3b2610c72ff/dqc_reference/reference_markers.fasta -out OceanDNA-b35376/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:14:51,181] [INFO] Task succeeded: Blastn
[2023-03-17 09:14:51,182] [INFO] Selected 29 target genomes.
[2023-03-17 09:14:51,182] [INFO] Target genome list was writen to OceanDNA-b35376/target_genomes.txt
[2023-03-17 09:14:51,279] [INFO] Task started: fastANI
[2023-03-17 09:14:51,279] [INFO] Running command: fastANI --query /var/lib/cwl/stge087f9f9-a840-4f96-a41c-61df311dee85/OceanDNA-b35376.fa --refList OceanDNA-b35376/target_genomes.txt --output OceanDNA-b35376/fastani_result.tsv --threads 1
[2023-03-17 09:15:10,101] [INFO] Task succeeded: fastANI
[2023-03-17 09:15:10,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1282cb7-3b72-46a7-9445-f3b2610c72ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:15:10,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1282cb7-3b72-46a7-9445-f3b2610c72ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:15:10,102] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:15:10,102] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:15:10,102] [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 09:15:10,102] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35376/tc_result.tsv
[2023-03-17 09:15:10,102] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:15:10,103] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:15:10,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1282cb7-3b72-46a7-9445-f3b2610c72ff/dqc_reference/checkm_data
[2023-03-17 09:15:10,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:15:10,233] [INFO] Task started: CheckM
[2023-03-17 09:15:10,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35376/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35376/checkm_input OceanDNA-b35376/checkm_result
[2023-03-17 09:16:01,666] [INFO] Task succeeded: CheckM
[2023-03-17 09:16:01,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 09:16:01,672] [INFO] ===== Completeness check finished =====
[2023-03-17 09:16:01,672] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:16:01,672] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35376/markers.fasta)
[2023-03-17 09:16:01,674] [INFO] Task started: Blastn
[2023-03-17 09:16:01,674] [INFO] Running command: blastn -query OceanDNA-b35376/markers.fasta -db /var/lib/cwl/stga1282cb7-3b72-46a7-9445-f3b2610c72ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35376/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:16:03,115] [INFO] Task succeeded: Blastn
[2023-03-17 09:16:03,117] [INFO] Selected 26 target genomes.
[2023-03-17 09:16:03,117] [INFO] Target genome list was writen to OceanDNA-b35376/target_genomes_gtdb.txt
[2023-03-17 09:16:04,338] [INFO] Task started: fastANI
[2023-03-17 09:16:04,338] [INFO] Running command: fastANI --query /var/lib/cwl/stge087f9f9-a840-4f96-a41c-61df311dee85/OceanDNA-b35376.fa --refList OceanDNA-b35376/target_genomes_gtdb.txt --output OceanDNA-b35376/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:16:20,132] [INFO] Task succeeded: fastANI
[2023-03-17 09:16:20,136] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:16:20,136] [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_009937625.1	s__GCA-001735895 sp009937625	77.5435	263	1131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__GCA-001735895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001735895.1	s__GCA-001735895 sp001735895	77.2152	211	1131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__GCA-001735895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494335.1	s__S144-22 sp015494335	77.0645	65	1131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__S144-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003231795.1	s__GCA-001735895 sp003231795	76.1056	89	1131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-001735895;f__GCA-001735895;g__GCA-001735895	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:16:20,137] [INFO] GTDB search result was written to OceanDNA-b35376/result_gtdb.tsv
[2023-03-17 09:16:20,137] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:16:20,138] [INFO] DFAST_QC result json was written to OceanDNA-b35376/dqc_result.json
[2023-03-17 09:16:20,138] [INFO] DFAST_QC completed!
[2023-03-17 09:16:20,138] [INFO] Total running time: 0h1m51s