[2023-03-18 02:48:47,727] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:48:47,727] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:48:47,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c5990aa-64a4-44ae-9612-7063bd21a893/dqc_reference
[2023-03-18 02:48:49,544] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:48:49,545] [INFO] Task started: Prodigal
[2023-03-18 02:48:49,545] [INFO] Running command: cat /var/lib/cwl/stg15ed4e80-c116-4fcd-a624-b9991d90d7e3/OceanDNA-b17710.fa | prodigal -d OceanDNA-b17710/cds.fna -a OceanDNA-b17710/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:49:02,627] [INFO] Task succeeded: Prodigal
[2023-03-18 02:49:02,627] [INFO] Task started: HMMsearch
[2023-03-18 02:49:02,627] [INFO] Running command: hmmsearch --tblout OceanDNA-b17710/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c5990aa-64a4-44ae-9612-7063bd21a893/dqc_reference/reference_markers.hmm OceanDNA-b17710/protein.faa > /dev/null
[2023-03-18 02:49:02,981] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:49:02,982] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg15ed4e80-c116-4fcd-a624-b9991d90d7e3/OceanDNA-b17710.fa]
[2023-03-18 02:49:03,028] [INFO] Query marker FASTA was written to OceanDNA-b17710/markers.fasta
[2023-03-18 02:49:03,030] [INFO] Task started: Blastn
[2023-03-18 02:49:03,030] [INFO] Running command: blastn -query OceanDNA-b17710/markers.fasta -db /var/lib/cwl/stg5c5990aa-64a4-44ae-9612-7063bd21a893/dqc_reference/reference_markers.fasta -out OceanDNA-b17710/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:03,639] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:03,640] [INFO] Selected 24 target genomes.
[2023-03-18 02:49:03,640] [INFO] Target genome list was writen to OceanDNA-b17710/target_genomes.txt
[2023-03-18 02:49:03,657] [INFO] Task started: fastANI
[2023-03-18 02:49:03,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg15ed4e80-c116-4fcd-a624-b9991d90d7e3/OceanDNA-b17710.fa --refList OceanDNA-b17710/target_genomes.txt --output OceanDNA-b17710/fastani_result.tsv --threads 1
[2023-03-18 02:49:21,207] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:21,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c5990aa-64a4-44ae-9612-7063bd21a893/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:49:21,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c5990aa-64a4-44ae-9612-7063bd21a893/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:49:21,208] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:49:21,208] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:49:21,208] [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
--------------------------------------------------------------------------------
[2023-03-18 02:49:21,208] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17710/tc_result.tsv
[2023-03-18 02:49:21,209] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:49:21,209] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:49:21,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c5990aa-64a4-44ae-9612-7063bd21a893/dqc_reference/checkm_data
[2023-03-18 02:49:21,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:49:21,216] [INFO] Task started: CheckM
[2023-03-18 02:49:21,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17710/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17710/checkm_input OceanDNA-b17710/checkm_result
[2023-03-18 02:49:57,609] [INFO] Task succeeded: CheckM
[2023-03-18 02:49:57,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.27%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:49:57,613] [INFO] ===== Completeness check finished =====
[2023-03-18 02:49:57,613] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:49:57,613] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17710/markers.fasta)
[2023-03-18 02:49:57,614] [INFO] Task started: Blastn
[2023-03-18 02:49:57,615] [INFO] Running command: blastn -query OceanDNA-b17710/markers.fasta -db /var/lib/cwl/stg5c5990aa-64a4-44ae-9612-7063bd21a893/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17710/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:58,420] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:58,421] [INFO] Selected 24 target genomes.
[2023-03-18 02:49:58,422] [INFO] Target genome list was writen to OceanDNA-b17710/target_genomes_gtdb.txt
[2023-03-18 02:49:58,531] [INFO] Task started: fastANI
[2023-03-18 02:49:58,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg15ed4e80-c116-4fcd-a624-b9991d90d7e3/OceanDNA-b17710.fa --refList OceanDNA-b17710/target_genomes_gtdb.txt --output OceanDNA-b17710/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:50:15,038] [INFO] Task succeeded: fastANI
[2023-03-18 02:50:15,038] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:50:15,038] [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
--------------------------------------------------------------------------------
[2023-03-18 02:50:15,038] [INFO] GTDB search result was written to OceanDNA-b17710/result_gtdb.tsv
[2023-03-18 02:50:15,039] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:50:15,039] [INFO] DFAST_QC result json was written to OceanDNA-b17710/dqc_result.json
[2023-03-18 02:50:15,039] [INFO] DFAST_QC completed!
[2023-03-18 02:50:15,039] [INFO] Total running time: 0h1m27s