[2023-03-14 12:25:41,477] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,478] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,478] [INFO] DQC Reference Directory: /var/lib/cwl/stg07894c48-55b6-4339-a6ee-82c82425fa53/dqc_reference
[2023-03-14 12:25:42,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,598] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,598] [INFO] Running command: cat /var/lib/cwl/stgb0bf6278-9c0e-4fc3-b3ef-ac1cc18e3c0d/OceanDNA-b40437.fa | prodigal -d OceanDNA-b40437/cds.fna -a OceanDNA-b40437/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:25:49,220] [INFO] Task succeeded: Prodigal
[2023-03-14 12:25:49,220] [INFO] Task started: HMMsearch
[2023-03-14 12:25:49,220] [INFO] Running command: hmmsearch --tblout OceanDNA-b40437/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07894c48-55b6-4339-a6ee-82c82425fa53/dqc_reference/reference_markers.hmm OceanDNA-b40437/protein.faa > /dev/null
[2023-03-14 12:25:49,374] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:25:49,374] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb0bf6278-9c0e-4fc3-b3ef-ac1cc18e3c0d/OceanDNA-b40437.fa]
[2023-03-14 12:25:49,388] [INFO] Query marker FASTA was written to OceanDNA-b40437/markers.fasta
[2023-03-14 12:25:49,389] [INFO] Task started: Blastn
[2023-03-14 12:25:49,389] [INFO] Running command: blastn -query OceanDNA-b40437/markers.fasta -db /var/lib/cwl/stg07894c48-55b6-4339-a6ee-82c82425fa53/dqc_reference/reference_markers.fasta -out OceanDNA-b40437/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:25:49,845] [INFO] Task succeeded: Blastn
[2023-03-14 12:25:49,846] [INFO] Selected 20 target genomes.
[2023-03-14 12:25:49,846] [INFO] Target genome list was writen to OceanDNA-b40437/target_genomes.txt
[2023-03-14 12:25:49,859] [INFO] Task started: fastANI
[2023-03-14 12:25:49,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0bf6278-9c0e-4fc3-b3ef-ac1cc18e3c0d/OceanDNA-b40437.fa --refList OceanDNA-b40437/target_genomes.txt --output OceanDNA-b40437/fastani_result.tsv --threads 1
[2023-03-14 12:26:02,158] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:02,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07894c48-55b6-4339-a6ee-82c82425fa53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:26:02,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07894c48-55b6-4339-a6ee-82c82425fa53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:26:02,158] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:26:02,159] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:26:02,159] [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
--------------------------------------------------------------------------------
[2023-03-14 12:26:02,159] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40437/tc_result.tsv
[2023-03-14 12:26:02,159] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:26:02,159] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:26:02,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07894c48-55b6-4339-a6ee-82c82425fa53/dqc_reference/checkm_data
[2023-03-14 12:26:02,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:26:02,172] [INFO] Task started: CheckM
[2023-03-14 12:26:02,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40437/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40437/checkm_input OceanDNA-b40437/checkm_result
[2023-03-14 12:26:25,074] [INFO] Task succeeded: CheckM
[2023-03-14 12:26:25,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:26:25,076] [INFO] ===== Completeness check finished =====
[2023-03-14 12:26:25,076] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:26:25,076] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40437/markers.fasta)
[2023-03-14 12:26:25,078] [INFO] Task started: Blastn
[2023-03-14 12:26:25,078] [INFO] Running command: blastn -query OceanDNA-b40437/markers.fasta -db /var/lib/cwl/stg07894c48-55b6-4339-a6ee-82c82425fa53/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40437/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:25,561] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:25,562] [INFO] Selected 18 target genomes.
[2023-03-14 12:26:25,562] [INFO] Target genome list was writen to OceanDNA-b40437/target_genomes_gtdb.txt
[2023-03-14 12:26:25,584] [INFO] Task started: fastANI
[2023-03-14 12:26:25,584] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0bf6278-9c0e-4fc3-b3ef-ac1cc18e3c0d/OceanDNA-b40437.fa --refList OceanDNA-b40437/target_genomes_gtdb.txt --output OceanDNA-b40437/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:26:36,282] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:36,285] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:26:36,285] [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_004535785.1	s__Pseudohongiella sp004535785	80.1371	139	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422225.1	s__Pseudohongiella sp002422225	79.3828	100	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711845.1	s__Pseudohongiella sp002711845	76.7012	52	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:26:36,285] [INFO] GTDB search result was written to OceanDNA-b40437/result_gtdb.tsv
[2023-03-14 12:26:36,285] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:26:36,286] [INFO] DFAST_QC result json was written to OceanDNA-b40437/dqc_result.json
[2023-03-14 12:26:36,286] [INFO] DFAST_QC completed!
[2023-03-14 12:26:36,286] [INFO] Total running time: 0h0m55s