[2023-03-19 02:57:44,683] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:57:44,683] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:57:44,683] [INFO] DQC Reference Directory: /var/lib/cwl/stgab0858b2-5664-40bc-b832-ce333b26b28a/dqc_reference
[2023-03-19 02:57:45,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:57:45,758] [INFO] Task started: Prodigal
[2023-03-19 02:57:45,758] [INFO] Running command: cat /var/lib/cwl/stgc0e33e36-9ba1-4aba-b9c6-1ef6811ce83d/OceanDNA-b46908.fa | prodigal -d OceanDNA-b46908/cds.fna -a OceanDNA-b46908/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:58:20,870] [INFO] Task succeeded: Prodigal
[2023-03-19 02:58:20,870] [INFO] Task started: HMMsearch
[2023-03-19 02:58:20,870] [INFO] Running command: hmmsearch --tblout OceanDNA-b46908/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab0858b2-5664-40bc-b832-ce333b26b28a/dqc_reference/reference_markers.hmm OceanDNA-b46908/protein.faa > /dev/null
[2023-03-19 02:58:21,088] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:58:21,089] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc0e33e36-9ba1-4aba-b9c6-1ef6811ce83d/OceanDNA-b46908.fa]
[2023-03-19 02:58:21,126] [INFO] Query marker FASTA was written to OceanDNA-b46908/markers.fasta
[2023-03-19 02:58:21,127] [INFO] Task started: Blastn
[2023-03-19 02:58:21,127] [INFO] Running command: blastn -query OceanDNA-b46908/markers.fasta -db /var/lib/cwl/stgab0858b2-5664-40bc-b832-ce333b26b28a/dqc_reference/reference_markers.fasta -out OceanDNA-b46908/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:58:21,621] [INFO] Task succeeded: Blastn
[2023-03-19 02:58:21,622] [INFO] Selected 15 target genomes.
[2023-03-19 02:58:21,623] [INFO] Target genome list was writen to OceanDNA-b46908/target_genomes.txt
[2023-03-19 02:58:21,657] [INFO] Task started: fastANI
[2023-03-19 02:58:21,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0e33e36-9ba1-4aba-b9c6-1ef6811ce83d/OceanDNA-b46908.fa --refList OceanDNA-b46908/target_genomes.txt --output OceanDNA-b46908/fastani_result.tsv --threads 1
[2023-03-19 02:58:34,050] [INFO] Task succeeded: fastANI
[2023-03-19 02:58:34,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab0858b2-5664-40bc-b832-ce333b26b28a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:58:34,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab0858b2-5664-40bc-b832-ce333b26b28a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:58:34,051] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:58:34,051] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:58:34,051] [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
--------------------------------------------------------------------------------
[2023-03-19 02:58:34,052] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46908/tc_result.tsv
[2023-03-19 02:58:34,052] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:58:34,052] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:58:34,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab0858b2-5664-40bc-b832-ce333b26b28a/dqc_reference/checkm_data
[2023-03-19 02:58:34,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:58:34,062] [INFO] Task started: CheckM
[2023-03-19 02:58:34,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46908/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46908/checkm_input OceanDNA-b46908/checkm_result
[2023-03-19 03:00:02,766] [INFO] Task succeeded: CheckM
[2023-03-19 03:00:02,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.97%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:00:02,774] [INFO] ===== Completeness check finished =====
[2023-03-19 03:00:02,774] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:00:02,775] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46908/markers.fasta)
[2023-03-19 03:00:02,775] [INFO] Task started: Blastn
[2023-03-19 03:00:02,775] [INFO] Running command: blastn -query OceanDNA-b46908/markers.fasta -db /var/lib/cwl/stgab0858b2-5664-40bc-b832-ce333b26b28a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46908/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:00:03,237] [INFO] Task succeeded: Blastn
[2023-03-19 03:00:03,240] [INFO] Selected 17 target genomes.
[2023-03-19 03:00:03,240] [INFO] Target genome list was writen to OceanDNA-b46908/target_genomes_gtdb.txt
[2023-03-19 03:00:03,255] [INFO] Task started: fastANI
[2023-03-19 03:00:03,256] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0e33e36-9ba1-4aba-b9c6-1ef6811ce83d/OceanDNA-b46908.fa --refList OceanDNA-b46908/target_genomes_gtdb.txt --output OceanDNA-b46908/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:00:15,126] [INFO] Task succeeded: fastANI
[2023-03-19 03:00:15,127] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:00:15,127] [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
--------------------------------------------------------------------------------
[2023-03-19 03:00:15,128] [INFO] GTDB search result was written to OceanDNA-b46908/result_gtdb.tsv
[2023-03-19 03:00:15,128] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:00:15,129] [INFO] DFAST_QC result json was written to OceanDNA-b46908/dqc_result.json
[2023-03-19 03:00:15,129] [INFO] DFAST_QC completed!
[2023-03-19 03:00:15,129] [INFO] Total running time: 0h2m30s