[2023-03-17 06:30:49,108] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,108] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,108] [INFO] DQC Reference Directory: /var/lib/cwl/stgb28d36e5-2a81-47de-a0ba-a2936b9f3d25/dqc_reference
[2023-03-17 06:30:50,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:50,293] [INFO] Task started: Prodigal
[2023-03-17 06:30:50,293] [INFO] Running command: cat /var/lib/cwl/stg438d9efe-49a7-4e09-ad34-9d190865eaaf/OceanDNA-b21782.fa | prodigal -d OceanDNA-b21782/cds.fna -a OceanDNA-b21782/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:30:55,382] [INFO] Task succeeded: Prodigal
[2023-03-17 06:30:55,382] [INFO] Task started: HMMsearch
[2023-03-17 06:30:55,382] [INFO] Running command: hmmsearch --tblout OceanDNA-b21782/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb28d36e5-2a81-47de-a0ba-a2936b9f3d25/dqc_reference/reference_markers.hmm OceanDNA-b21782/protein.faa > /dev/null
[2023-03-17 06:30:55,515] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:30:55,516] [INFO] Found 6/6 markers.
[2023-03-17 06:30:55,522] [INFO] Query marker FASTA was written to OceanDNA-b21782/markers.fasta
[2023-03-17 06:30:55,522] [INFO] Task started: Blastn
[2023-03-17 06:30:55,522] [INFO] Running command: blastn -query OceanDNA-b21782/markers.fasta -db /var/lib/cwl/stgb28d36e5-2a81-47de-a0ba-a2936b9f3d25/dqc_reference/reference_markers.fasta -out OceanDNA-b21782/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:30:56,017] [INFO] Task succeeded: Blastn
[2023-03-17 06:30:56,018] [INFO] Selected 16 target genomes.
[2023-03-17 06:30:56,018] [INFO] Target genome list was writen to OceanDNA-b21782/target_genomes.txt
[2023-03-17 06:30:56,026] [INFO] Task started: fastANI
[2023-03-17 06:30:56,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg438d9efe-49a7-4e09-ad34-9d190865eaaf/OceanDNA-b21782.fa --refList OceanDNA-b21782/target_genomes.txt --output OceanDNA-b21782/fastani_result.tsv --threads 1
[2023-03-17 06:31:07,018] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:07,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb28d36e5-2a81-47de-a0ba-a2936b9f3d25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:07,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb28d36e5-2a81-47de-a0ba-a2936b9f3d25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:07,019] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:07,019] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 06:31:07,019] [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 06:31:07,019] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21782/tc_result.tsv
[2023-03-17 06:31:07,019] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:07,019] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:07,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb28d36e5-2a81-47de-a0ba-a2936b9f3d25/dqc_reference/checkm_data
[2023-03-17 06:31:07,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:07,024] [INFO] Task started: CheckM
[2023-03-17 06:31:07,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21782/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21782/checkm_input OceanDNA-b21782/checkm_result
[2023-03-17 06:31:26,139] [INFO] Task succeeded: CheckM
[2023-03-17 06:31:26,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:31:26,141] [INFO] ===== Completeness check finished =====
[2023-03-17 06:31:26,141] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:31:26,141] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21782/markers.fasta)
[2023-03-17 06:31:26,142] [INFO] Task started: Blastn
[2023-03-17 06:31:26,142] [INFO] Running command: blastn -query OceanDNA-b21782/markers.fasta -db /var/lib/cwl/stgb28d36e5-2a81-47de-a0ba-a2936b9f3d25/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21782/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:26,825] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:26,826] [INFO] Selected 25 target genomes.
[2023-03-17 06:31:26,826] [INFO] Target genome list was writen to OceanDNA-b21782/target_genomes_gtdb.txt
[2023-03-17 06:31:27,382] [INFO] Task started: fastANI
[2023-03-17 06:31:27,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg438d9efe-49a7-4e09-ad34-9d190865eaaf/OceanDNA-b21782.fa --refList OceanDNA-b21782/target_genomes_gtdb.txt --output OceanDNA-b21782/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:31:35,088] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:35,088] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:31:35,089] [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
--------------------------------------------------------------------------------
[2023-03-17 06:31:35,089] [INFO] GTDB search result was written to OceanDNA-b21782/result_gtdb.tsv
[2023-03-17 06:31:35,089] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:31:35,089] [INFO] DFAST_QC result json was written to OceanDNA-b21782/dqc_result.json
[2023-03-17 06:31:35,089] [INFO] DFAST_QC completed!
[2023-03-17 06:31:35,089] [INFO] Total running time: 0h0m46s