[2023-03-19 04:49:27,625] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:49:27,626] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:49:27,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f4df077-fc6f-4cf5-99b5-702c928941ca/dqc_reference
[2023-03-19 04:49:28,749] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:49:28,750] [INFO] Task started: Prodigal
[2023-03-19 04:49:28,750] [INFO] Running command: cat /var/lib/cwl/stge9436ee0-f49e-4f09-82c2-d846d8f1889d/OceanDNA-b22314.fa | prodigal -d OceanDNA-b22314/cds.fna -a OceanDNA-b22314/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:50:17,058] [INFO] Task succeeded: Prodigal
[2023-03-19 04:50:17,058] [INFO] Task started: HMMsearch
[2023-03-19 04:50:17,058] [INFO] Running command: hmmsearch --tblout OceanDNA-b22314/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f4df077-fc6f-4cf5-99b5-702c928941ca/dqc_reference/reference_markers.hmm OceanDNA-b22314/protein.faa > /dev/null
[2023-03-19 04:50:17,373] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:50:17,374] [INFO] Found 6/6 markers.
[2023-03-19 04:50:17,430] [INFO] Query marker FASTA was written to OceanDNA-b22314/markers.fasta
[2023-03-19 04:50:17,431] [INFO] Task started: Blastn
[2023-03-19 04:50:17,431] [INFO] Running command: blastn -query OceanDNA-b22314/markers.fasta -db /var/lib/cwl/stg0f4df077-fc6f-4cf5-99b5-702c928941ca/dqc_reference/reference_markers.fasta -out OceanDNA-b22314/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:50:17,981] [INFO] Task succeeded: Blastn
[2023-03-19 04:50:17,982] [INFO] Selected 12 target genomes.
[2023-03-19 04:50:17,983] [INFO] Target genome list was writen to OceanDNA-b22314/target_genomes.txt
[2023-03-19 04:50:17,991] [INFO] Task started: fastANI
[2023-03-19 04:50:17,991] [INFO] Running command: fastANI --query /var/lib/cwl/stge9436ee0-f49e-4f09-82c2-d846d8f1889d/OceanDNA-b22314.fa --refList OceanDNA-b22314/target_genomes.txt --output OceanDNA-b22314/fastani_result.tsv --threads 1
[2023-03-19 04:50:29,011] [INFO] Task succeeded: fastANI
[2023-03-19 04:50:29,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f4df077-fc6f-4cf5-99b5-702c928941ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:50:29,012] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f4df077-fc6f-4cf5-99b5-702c928941ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:50:29,012] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:50:29,012] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:50:29,012] [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 04:50:29,012] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22314/tc_result.tsv
[2023-03-19 04:50:29,012] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:50:29,012] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:50:29,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f4df077-fc6f-4cf5-99b5-702c928941ca/dqc_reference/checkm_data
[2023-03-19 04:50:29,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:50:29,025] [INFO] Task started: CheckM
[2023-03-19 04:50:29,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22314/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22314/checkm_input OceanDNA-b22314/checkm_result
[2023-03-19 04:52:26,104] [INFO] Task succeeded: CheckM
[2023-03-19 04:52:26,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:52:26,137] [INFO] ===== Completeness check finished =====
[2023-03-19 04:52:26,137] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:52:26,137] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22314/markers.fasta)
[2023-03-19 04:52:26,139] [INFO] Task started: Blastn
[2023-03-19 04:52:26,139] [INFO] Running command: blastn -query OceanDNA-b22314/markers.fasta -db /var/lib/cwl/stg0f4df077-fc6f-4cf5-99b5-702c928941ca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22314/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:52:27,016] [INFO] Task succeeded: Blastn
[2023-03-19 04:52:27,017] [INFO] Selected 23 target genomes.
[2023-03-19 04:52:27,017] [INFO] Target genome list was writen to OceanDNA-b22314/target_genomes_gtdb.txt
[2023-03-19 04:52:27,057] [INFO] Task started: fastANI
[2023-03-19 04:52:27,057] [INFO] Running command: fastANI --query /var/lib/cwl/stge9436ee0-f49e-4f09-82c2-d846d8f1889d/OceanDNA-b22314.fa --refList OceanDNA-b22314/target_genomes_gtdb.txt --output OceanDNA-b22314/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:52:41,936] [INFO] Task succeeded: fastANI
[2023-03-19 04:52:41,937] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:52:41,937] [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 04:52:41,937] [INFO] GTDB search result was written to OceanDNA-b22314/result_gtdb.tsv
[2023-03-19 04:52:41,937] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:52:41,938] [INFO] DFAST_QC result json was written to OceanDNA-b22314/dqc_result.json
[2023-03-19 04:52:41,938] [INFO] DFAST_QC completed!
[2023-03-19 04:52:41,938] [INFO] Total running time: 0h3m14s