[2023-03-16 00:43:24,333] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:43:24,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:43:24,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg72116c2b-821a-43c9-8658-c561f10d9730/dqc_reference
[2023-03-16 00:43:25,486] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:43:25,486] [INFO] Task started: Prodigal
[2023-03-16 00:43:25,486] [INFO] Running command: cat /var/lib/cwl/stg224fcd79-021d-4d1f-b335-fbfad348164d/OceanDNA-b35769.fa | prodigal -d OceanDNA-b35769/cds.fna -a OceanDNA-b35769/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:43:37,998] [INFO] Task succeeded: Prodigal
[2023-03-16 00:43:37,998] [INFO] Task started: HMMsearch
[2023-03-16 00:43:37,998] [INFO] Running command: hmmsearch --tblout OceanDNA-b35769/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72116c2b-821a-43c9-8658-c561f10d9730/dqc_reference/reference_markers.hmm OceanDNA-b35769/protein.faa > /dev/null
[2023-03-16 00:43:38,185] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:43:38,185] [INFO] Found 6/6 markers.
[2023-03-16 00:43:38,215] [INFO] Query marker FASTA was written to OceanDNA-b35769/markers.fasta
[2023-03-16 00:43:38,216] [INFO] Task started: Blastn
[2023-03-16 00:43:38,216] [INFO] Running command: blastn -query OceanDNA-b35769/markers.fasta -db /var/lib/cwl/stg72116c2b-821a-43c9-8658-c561f10d9730/dqc_reference/reference_markers.fasta -out OceanDNA-b35769/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:43:38,801] [INFO] Task succeeded: Blastn
[2023-03-16 00:43:38,809] [INFO] Selected 31 target genomes.
[2023-03-16 00:43:38,809] [INFO] Target genome list was writen to OceanDNA-b35769/target_genomes.txt
[2023-03-16 00:43:38,838] [INFO] Task started: fastANI
[2023-03-16 00:43:38,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg224fcd79-021d-4d1f-b335-fbfad348164d/OceanDNA-b35769.fa --refList OceanDNA-b35769/target_genomes.txt --output OceanDNA-b35769/fastani_result.tsv --threads 1
[2023-03-16 00:43:55,679] [INFO] Task succeeded: fastANI
[2023-03-16 00:43:55,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72116c2b-821a-43c9-8658-c561f10d9730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:43:55,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72116c2b-821a-43c9-8658-c561f10d9730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:43:55,679] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:43:55,679] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:43:55,679] [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 00:43:55,684] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35769/tc_result.tsv
[2023-03-16 00:43:55,693] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:43:55,693] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:43:55,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72116c2b-821a-43c9-8658-c561f10d9730/dqc_reference/checkm_data
[2023-03-16 00:43:55,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:43:55,833] [INFO] Task started: CheckM
[2023-03-16 00:43:55,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35769/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35769/checkm_input OceanDNA-b35769/checkm_result
[2023-03-16 00:44:30,704] [INFO] Task succeeded: CheckM
[2023-03-16 00:44:30,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:44:30,721] [INFO] ===== Completeness check finished =====
[2023-03-16 00:44:30,721] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:44:30,721] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35769/markers.fasta)
[2023-03-16 00:44:30,722] [INFO] Task started: Blastn
[2023-03-16 00:44:30,722] [INFO] Running command: blastn -query OceanDNA-b35769/markers.fasta -db /var/lib/cwl/stg72116c2b-821a-43c9-8658-c561f10d9730/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35769/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:44:31,649] [INFO] Task succeeded: Blastn
[2023-03-16 00:44:31,666] [INFO] Selected 31 target genomes.
[2023-03-16 00:44:31,666] [INFO] Target genome list was writen to OceanDNA-b35769/target_genomes_gtdb.txt
[2023-03-16 00:44:31,746] [INFO] Task started: fastANI
[2023-03-16 00:44:31,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg224fcd79-021d-4d1f-b335-fbfad348164d/OceanDNA-b35769.fa --refList OceanDNA-b35769/target_genomes_gtdb.txt --output OceanDNA-b35769/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:44:45,805] [INFO] Task succeeded: fastANI
[2023-03-16 00:44:45,809] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:44:45,809] [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_013151045.1	s__GCA-2400775 sp013151045	77.1159	138	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2400775;f__GCA-2400775;g__GCA-2400775	95.0	95.23	95.23	0.83	0.83	2	-
GCA_002400905.2	s__GCA-2400775 sp002400905	77.0971	124	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2400775;f__GCA-2400775;g__GCA-2400775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015492075.1	s__GCA-2400775 sp015492075	76.9755	103	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2400775;f__GCA-2400775;g__GCA-2400775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400775.1	s__GCA-2400775 sp002400775	76.9687	54	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2400775;f__GCA-2400775;g__GCA-2400775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765075.1	s__GCA-2400775 sp016765075	76.6175	101	764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2400775;f__GCA-2400775;g__GCA-2400775	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:44:45,815] [INFO] GTDB search result was written to OceanDNA-b35769/result_gtdb.tsv
[2023-03-16 00:44:45,828] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:44:45,834] [INFO] DFAST_QC result json was written to OceanDNA-b35769/dqc_result.json
[2023-03-16 00:44:45,834] [INFO] DFAST_QC completed!
[2023-03-16 00:44:45,834] [INFO] Total running time: 0h1m22s