[2023-03-14 14:35:17,468] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:35:17,468] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:35:17,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg67713318-7151-4c05-b8ef-97bf353aa992/dqc_reference
[2023-03-14 14:35:20,301] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:35:20,302] [INFO] Task started: Prodigal
[2023-03-14 14:35:20,302] [INFO] Running command: cat /var/lib/cwl/stgf8d0ccd5-15d3-4989-ac95-1e8f16274b90/OceanDNA-b45634.fa | prodigal -d OceanDNA-b45634/cds.fna -a OceanDNA-b45634/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:35:36,175] [INFO] Task succeeded: Prodigal
[2023-03-14 14:35:36,176] [INFO] Task started: HMMsearch
[2023-03-14 14:35:36,176] [INFO] Running command: hmmsearch --tblout OceanDNA-b45634/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67713318-7151-4c05-b8ef-97bf353aa992/dqc_reference/reference_markers.hmm OceanDNA-b45634/protein.faa > /dev/null
[2023-03-14 14:35:36,345] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:35:36,346] [INFO] Found 6/6 markers.
[2023-03-14 14:35:36,366] [INFO] Query marker FASTA was written to OceanDNA-b45634/markers.fasta
[2023-03-14 14:35:36,367] [INFO] Task started: Blastn
[2023-03-14 14:35:36,367] [INFO] Running command: blastn -query OceanDNA-b45634/markers.fasta -db /var/lib/cwl/stg67713318-7151-4c05-b8ef-97bf353aa992/dqc_reference/reference_markers.fasta -out OceanDNA-b45634/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:35:36,921] [INFO] Task succeeded: Blastn
[2023-03-14 14:35:36,922] [INFO] Selected 14 target genomes.
[2023-03-14 14:35:36,923] [INFO] Target genome list was writen to OceanDNA-b45634/target_genomes.txt
[2023-03-14 14:35:36,931] [INFO] Task started: fastANI
[2023-03-14 14:35:36,931] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8d0ccd5-15d3-4989-ac95-1e8f16274b90/OceanDNA-b45634.fa --refList OceanDNA-b45634/target_genomes.txt --output OceanDNA-b45634/fastani_result.tsv --threads 1
[2023-03-14 14:35:42,672] [INFO] Task succeeded: fastANI
[2023-03-14 14:35:42,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67713318-7151-4c05-b8ef-97bf353aa992/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:35:42,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67713318-7151-4c05-b8ef-97bf353aa992/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:35:42,673] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:35:42,673] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:35:42,673] [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 14:35:42,673] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45634/tc_result.tsv
[2023-03-14 14:35:42,673] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:35:42,673] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:35:42,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67713318-7151-4c05-b8ef-97bf353aa992/dqc_reference/checkm_data
[2023-03-14 14:35:42,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:35:42,682] [INFO] Task started: CheckM
[2023-03-14 14:35:42,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45634/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45634/checkm_input OceanDNA-b45634/checkm_result
[2023-03-14 14:36:38,135] [INFO] Task succeeded: CheckM
[2023-03-14 14:36:38,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.59%
Contamintation: 0.84%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:36:38,139] [INFO] ===== Completeness check finished =====
[2023-03-14 14:36:38,139] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:36:38,139] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45634/markers.fasta)
[2023-03-14 14:36:38,140] [INFO] Task started: Blastn
[2023-03-14 14:36:38,140] [INFO] Running command: blastn -query OceanDNA-b45634/markers.fasta -db /var/lib/cwl/stg67713318-7151-4c05-b8ef-97bf353aa992/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45634/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:36:38,873] [INFO] Task succeeded: Blastn
[2023-03-14 14:36:38,874] [INFO] Selected 22 target genomes.
[2023-03-14 14:36:38,874] [INFO] Target genome list was writen to OceanDNA-b45634/target_genomes_gtdb.txt
[2023-03-14 14:36:38,889] [INFO] Task started: fastANI
[2023-03-14 14:36:38,889] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8d0ccd5-15d3-4989-ac95-1e8f16274b90/OceanDNA-b45634.fa --refList OceanDNA-b45634/target_genomes_gtdb.txt --output OceanDNA-b45634/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:36:47,790] [INFO] Task succeeded: fastANI
[2023-03-14 14:36:47,794] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:36:47,794] [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_018646565.1	s__MB11C04 sp018646565	80.2649	162	593	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478775.1	s__MB11C04 sp002477515	79.5086	248	593	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.93	98.38	0.86	0.80	5	-
GCA_018645475.1	s__MB11C04 sp018645475	77.9065	138	593	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018675995.1	s__MB11C04 sp018675995	77.6152	87	593	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902580225.1	s__MB11C04 sp902580225	77.0718	83	593	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:36:47,794] [INFO] GTDB search result was written to OceanDNA-b45634/result_gtdb.tsv
[2023-03-14 14:36:47,794] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:36:47,795] [INFO] DFAST_QC result json was written to OceanDNA-b45634/dqc_result.json
[2023-03-14 14:36:47,796] [INFO] DFAST_QC completed!
[2023-03-14 14:36:47,796] [INFO] Total running time: 0h1m30s