[2023-03-16 04:20:43,514] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:20:43,515] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:20:43,515] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1c01032-fc82-4a7e-92f7-f82cd8f7f068/dqc_reference
[2023-03-16 04:20:44,653] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:20:44,653] [INFO] Task started: Prodigal
[2023-03-16 04:20:44,653] [INFO] Running command: cat /var/lib/cwl/stg2edcac78-9843-4288-b663-05935ea02383/OceanDNA-b35536.fa | prodigal -d OceanDNA-b35536/cds.fna -a OceanDNA-b35536/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:20:47,882] [INFO] Task succeeded: Prodigal
[2023-03-16 04:20:47,882] [INFO] Task started: HMMsearch
[2023-03-16 04:20:47,883] [INFO] Running command: hmmsearch --tblout OceanDNA-b35536/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1c01032-fc82-4a7e-92f7-f82cd8f7f068/dqc_reference/reference_markers.hmm OceanDNA-b35536/protein.faa > /dev/null
[2023-03-16 04:20:48,094] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:20:48,095] [INFO] Found 6/6 markers.
[2023-03-16 04:20:48,101] [INFO] Query marker FASTA was written to OceanDNA-b35536/markers.fasta
[2023-03-16 04:20:48,103] [INFO] Task started: Blastn
[2023-03-16 04:20:48,103] [INFO] Running command: blastn -query OceanDNA-b35536/markers.fasta -db /var/lib/cwl/stgb1c01032-fc82-4a7e-92f7-f82cd8f7f068/dqc_reference/reference_markers.fasta -out OceanDNA-b35536/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:20:48,879] [INFO] Task succeeded: Blastn
[2023-03-16 04:20:48,880] [INFO] Selected 11 target genomes.
[2023-03-16 04:20:48,880] [INFO] Target genome list was writen to OceanDNA-b35536/target_genomes.txt
[2023-03-16 04:20:48,886] [INFO] Task started: fastANI
[2023-03-16 04:20:48,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg2edcac78-9843-4288-b663-05935ea02383/OceanDNA-b35536.fa --refList OceanDNA-b35536/target_genomes.txt --output OceanDNA-b35536/fastani_result.tsv --threads 1
[2023-03-16 04:20:53,121] [INFO] Task succeeded: fastANI
[2023-03-16 04:20:53,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1c01032-fc82-4a7e-92f7-f82cd8f7f068/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:20:53,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1c01032-fc82-4a7e-92f7-f82cd8f7f068/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:20:53,122] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:20:53,122] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:20:53,122] [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
--------------------------------------------------------------------------------
[2023-03-16 04:20:53,122] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35536/tc_result.tsv
[2023-03-16 04:20:53,122] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:20:53,122] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:20:53,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1c01032-fc82-4a7e-92f7-f82cd8f7f068/dqc_reference/checkm_data
[2023-03-16 04:20:53,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:20:53,177] [INFO] Task started: CheckM
[2023-03-16 04:20:53,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35536/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35536/checkm_input OceanDNA-b35536/checkm_result
[2023-03-16 04:21:12,297] [INFO] Task succeeded: CheckM
[2023-03-16 04:21:12,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:21:12,299] [INFO] ===== Completeness check finished =====
[2023-03-16 04:21:12,299] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:21:12,299] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35536/markers.fasta)
[2023-03-16 04:21:12,301] [INFO] Task started: Blastn
[2023-03-16 04:21:12,301] [INFO] Running command: blastn -query OceanDNA-b35536/markers.fasta -db /var/lib/cwl/stgb1c01032-fc82-4a7e-92f7-f82cd8f7f068/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35536/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:21:13,511] [INFO] Task succeeded: Blastn
[2023-03-16 04:21:13,512] [INFO] Selected 25 target genomes.
[2023-03-16 04:21:13,512] [INFO] Target genome list was writen to OceanDNA-b35536/target_genomes_gtdb.txt
[2023-03-16 04:21:13,572] [INFO] Task started: fastANI
[2023-03-16 04:21:13,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg2edcac78-9843-4288-b663-05935ea02383/OceanDNA-b35536.fa --refList OceanDNA-b35536/target_genomes_gtdb.txt --output OceanDNA-b35536/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:21:20,551] [INFO] Task succeeded: fastANI
[2023-03-16 04:21:20,555] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:21:20,555] [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_902521725.1	s__CACLCV01 sp902521725	79.7095	122	206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__CACLCV01	95.0	99.92	99.92	0.90	0.90	2	-
GCA_902535975.1	s__CACLCV01 sp902535975	79.425	98	206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__CACLCV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779485.1	s__CACLCV01 sp016779485	77.2149	52	206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__CACLCV01	95.0	99.98	99.97	0.94	0.91	3	-
GCA_902559355.1	s__CACLCV01 sp902559355	77.1302	56	206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__CACLCV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:21:20,555] [INFO] GTDB search result was written to OceanDNA-b35536/result_gtdb.tsv
[2023-03-16 04:21:20,555] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:21:20,556] [INFO] DFAST_QC result json was written to OceanDNA-b35536/dqc_result.json
[2023-03-16 04:21:20,556] [INFO] DFAST_QC completed!
[2023-03-16 04:21:20,556] [INFO] Total running time: 0h0m37s