[2023-03-16 20:36:14,513] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:36:14,513] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:36:14,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ab318e4-ec8f-4c31-86ab-db9f86b8e41d/dqc_reference
[2023-03-16 20:36:15,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:36:15,620] [INFO] Task started: Prodigal
[2023-03-16 20:36:15,621] [INFO] Running command: cat /var/lib/cwl/stgcc341aff-5a14-44f5-aa82-7277dc2f4a94/OceanDNA-b7332.fa | prodigal -d OceanDNA-b7332/cds.fna -a OceanDNA-b7332/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:36:23,691] [INFO] Task succeeded: Prodigal
[2023-03-16 20:36:23,692] [INFO] Task started: HMMsearch
[2023-03-16 20:36:23,692] [INFO] Running command: hmmsearch --tblout OceanDNA-b7332/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ab318e4-ec8f-4c31-86ab-db9f86b8e41d/dqc_reference/reference_markers.hmm OceanDNA-b7332/protein.faa > /dev/null
[2023-03-16 20:36:23,837] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:36:23,837] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcc341aff-5a14-44f5-aa82-7277dc2f4a94/OceanDNA-b7332.fa]
[2023-03-16 20:36:23,848] [INFO] Query marker FASTA was written to OceanDNA-b7332/markers.fasta
[2023-03-16 20:36:23,849] [INFO] Task started: Blastn
[2023-03-16 20:36:23,849] [INFO] Running command: blastn -query OceanDNA-b7332/markers.fasta -db /var/lib/cwl/stg9ab318e4-ec8f-4c31-86ab-db9f86b8e41d/dqc_reference/reference_markers.fasta -out OceanDNA-b7332/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:36:24,356] [INFO] Task succeeded: Blastn
[2023-03-16 20:36:24,356] [INFO] Selected 17 target genomes.
[2023-03-16 20:36:24,357] [INFO] Target genome list was writen to OceanDNA-b7332/target_genomes.txt
[2023-03-16 20:36:24,368] [INFO] Task started: fastANI
[2023-03-16 20:36:24,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc341aff-5a14-44f5-aa82-7277dc2f4a94/OceanDNA-b7332.fa --refList OceanDNA-b7332/target_genomes.txt --output OceanDNA-b7332/fastani_result.tsv --threads 1
[2023-03-16 20:36:34,549] [INFO] Task succeeded: fastANI
[2023-03-16 20:36:34,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ab318e4-ec8f-4c31-86ab-db9f86b8e41d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:36:34,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ab318e4-ec8f-4c31-86ab-db9f86b8e41d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:36:34,550] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:36:34,550] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 20:36:34,550] [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 20:36:34,550] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7332/tc_result.tsv
[2023-03-16 20:36:34,550] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:36:34,550] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:36:34,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ab318e4-ec8f-4c31-86ab-db9f86b8e41d/dqc_reference/checkm_data
[2023-03-16 20:36:34,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:36:34,734] [INFO] Task started: CheckM
[2023-03-16 20:36:34,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7332/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7332/checkm_input OceanDNA-b7332/checkm_result
[2023-03-16 20:37:00,404] [INFO] Task succeeded: CheckM
[2023-03-16 20:37:00,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:37:00,406] [INFO] ===== Completeness check finished =====
[2023-03-16 20:37:00,407] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:37:00,407] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7332/markers.fasta)
[2023-03-16 20:37:00,408] [INFO] Task started: Blastn
[2023-03-16 20:37:00,408] [INFO] Running command: blastn -query OceanDNA-b7332/markers.fasta -db /var/lib/cwl/stg9ab318e4-ec8f-4c31-86ab-db9f86b8e41d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7332/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:37:01,061] [INFO] Task succeeded: Blastn
[2023-03-16 20:37:01,062] [INFO] Selected 7 target genomes.
[2023-03-16 20:37:01,062] [INFO] Target genome list was writen to OceanDNA-b7332/target_genomes_gtdb.txt
[2023-03-16 20:37:01,066] [INFO] Task started: fastANI
[2023-03-16 20:37:01,067] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc341aff-5a14-44f5-aa82-7277dc2f4a94/OceanDNA-b7332.fa --refList OceanDNA-b7332/target_genomes_gtdb.txt --output OceanDNA-b7332/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:37:04,246] [INFO] Task succeeded: fastANI
[2023-03-16 20:37:04,250] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 20:37:04,251] [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
GCF_001735745.1	s__Hel1-33-131 sp001735745	92.797	331	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	84.4319	286	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	83.6189	249	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	83.5111	278	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608735.1	s__Hel1-33-131 sp018608735	81.5895	219	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	80.7197	235	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 20:37:04,251] [INFO] GTDB search result was written to OceanDNA-b7332/result_gtdb.tsv
[2023-03-16 20:37:04,251] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:37:04,252] [INFO] DFAST_QC result json was written to OceanDNA-b7332/dqc_result.json
[2023-03-16 20:37:04,252] [INFO] DFAST_QC completed!
[2023-03-16 20:37:04,252] [INFO] Total running time: 0h0m50s