[2023-03-17 13:01:51,840] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,840] [INFO] DQC Reference Directory: /var/lib/cwl/stga3f9e0cb-6f07-452d-9ab8-2be058d9161b/dqc_reference
[2023-03-17 13:01:53,088] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:53,088] [INFO] Task started: Prodigal
[2023-03-17 13:01:53,089] [INFO] Running command: cat /var/lib/cwl/stgae88c104-6e48-43ae-8ad3-f38fdc6a3158/OceanDNA-b18556.fa | prodigal -d OceanDNA-b18556/cds.fna -a OceanDNA-b18556/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:03,504] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:03,504] [INFO] Task started: HMMsearch
[2023-03-17 13:02:03,504] [INFO] Running command: hmmsearch --tblout OceanDNA-b18556/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3f9e0cb-6f07-452d-9ab8-2be058d9161b/dqc_reference/reference_markers.hmm OceanDNA-b18556/protein.faa > /dev/null
[2023-03-17 13:02:03,720] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:03,721] [INFO] Found 6/6 markers.
[2023-03-17 13:02:03,741] [INFO] Query marker FASTA was written to OceanDNA-b18556/markers.fasta
[2023-03-17 13:02:03,741] [INFO] Task started: Blastn
[2023-03-17 13:02:03,741] [INFO] Running command: blastn -query OceanDNA-b18556/markers.fasta -db /var/lib/cwl/stga3f9e0cb-6f07-452d-9ab8-2be058d9161b/dqc_reference/reference_markers.fasta -out OceanDNA-b18556/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:04,256] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:04,257] [INFO] Selected 13 target genomes.
[2023-03-17 13:02:04,258] [INFO] Target genome list was writen to OceanDNA-b18556/target_genomes.txt
[2023-03-17 13:02:04,267] [INFO] Task started: fastANI
[2023-03-17 13:02:04,267] [INFO] Running command: fastANI --query /var/lib/cwl/stgae88c104-6e48-43ae-8ad3-f38fdc6a3158/OceanDNA-b18556.fa --refList OceanDNA-b18556/target_genomes.txt --output OceanDNA-b18556/fastani_result.tsv --threads 1
[2023-03-17 13:02:10,599] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:10,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3f9e0cb-6f07-452d-9ab8-2be058d9161b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:10,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3f9e0cb-6f07-452d-9ab8-2be058d9161b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:10,600] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:10,600] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 13:02:10,600] [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 13:02:10,601] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18556/tc_result.tsv
[2023-03-17 13:02:10,601] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:10,601] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:10,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3f9e0cb-6f07-452d-9ab8-2be058d9161b/dqc_reference/checkm_data
[2023-03-17 13:02:10,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:10,607] [INFO] Task started: CheckM
[2023-03-17 13:02:10,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18556/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18556/checkm_input OceanDNA-b18556/checkm_result
[2023-03-17 13:02:40,893] [INFO] Task succeeded: CheckM
[2023-03-17 13:02:40,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 13:02:40,895] [INFO] ===== Completeness check finished =====
[2023-03-17 13:02:40,895] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:02:40,895] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18556/markers.fasta)
[2023-03-17 13:02:40,895] [INFO] Task started: Blastn
[2023-03-17 13:02:40,896] [INFO] Running command: blastn -query OceanDNA-b18556/markers.fasta -db /var/lib/cwl/stga3f9e0cb-6f07-452d-9ab8-2be058d9161b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18556/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:41,635] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:41,636] [INFO] Selected 18 target genomes.
[2023-03-17 13:02:41,636] [INFO] Target genome list was writen to OceanDNA-b18556/target_genomes_gtdb.txt
[2023-03-17 13:02:42,104] [INFO] Task started: fastANI
[2023-03-17 13:02:42,104] [INFO] Running command: fastANI --query /var/lib/cwl/stgae88c104-6e48-43ae-8ad3-f38fdc6a3158/OceanDNA-b18556.fa --refList OceanDNA-b18556/target_genomes_gtdb.txt --output OceanDNA-b18556/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:02:48,016] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:48,019] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 13:02:48,019] [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_018651745.1	s__JAAZYX01 sp018651745	99.9768	582	603	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__JAAZYX01	95.0	99.98	99.94	0.97	0.95	16	conclusive
GCA_014239435.1	s__JAAZYX01 sp014239435	78.8808	244	603	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__JAAZYX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:02:48,019] [INFO] GTDB search result was written to OceanDNA-b18556/result_gtdb.tsv
[2023-03-17 13:02:48,020] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:02:48,020] [INFO] DFAST_QC result json was written to OceanDNA-b18556/dqc_result.json
[2023-03-17 13:02:48,020] [INFO] DFAST_QC completed!
[2023-03-17 13:02:48,020] [INFO] Total running time: 0h0m56s