[2023-03-16 02:38:05,045] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:05,045] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:05,045] [INFO] DQC Reference Directory: /var/lib/cwl/stgee712094-0284-4152-b760-423d6f91ebef/dqc_reference
[2023-03-16 02:38:06,332] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,332] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,333] [INFO] Running command: cat /var/lib/cwl/stg234e89d2-4248-40d8-896d-be98d2212694/OceanDNA-b12982.fa | prodigal -d OceanDNA-b12982/cds.fna -a OceanDNA-b12982/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:22,607] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:22,607] [INFO] Task started: HMMsearch
[2023-03-16 02:38:22,607] [INFO] Running command: hmmsearch --tblout OceanDNA-b12982/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee712094-0284-4152-b760-423d6f91ebef/dqc_reference/reference_markers.hmm OceanDNA-b12982/protein.faa > /dev/null
[2023-03-16 02:38:22,809] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:22,810] [INFO] Found 6/6 markers.
[2023-03-16 02:38:22,826] [INFO] Query marker FASTA was written to OceanDNA-b12982/markers.fasta
[2023-03-16 02:38:22,827] [INFO] Task started: Blastn
[2023-03-16 02:38:22,827] [INFO] Running command: blastn -query OceanDNA-b12982/markers.fasta -db /var/lib/cwl/stgee712094-0284-4152-b760-423d6f91ebef/dqc_reference/reference_markers.fasta -out OceanDNA-b12982/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:23,355] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:23,356] [INFO] Selected 29 target genomes.
[2023-03-16 02:38:23,356] [INFO] Target genome list was writen to OceanDNA-b12982/target_genomes.txt
[2023-03-16 02:38:23,373] [INFO] Task started: fastANI
[2023-03-16 02:38:23,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg234e89d2-4248-40d8-896d-be98d2212694/OceanDNA-b12982.fa --refList OceanDNA-b12982/target_genomes.txt --output OceanDNA-b12982/fastani_result.tsv --threads 1
[2023-03-16 02:38:44,733] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:44,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee712094-0284-4152-b760-423d6f91ebef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:44,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee712094-0284-4152-b760-423d6f91ebef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:44,734] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:44,734] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 02:38:44,734] [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 02:38:44,734] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12982/tc_result.tsv
[2023-03-16 02:38:44,734] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:44,734] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:44,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee712094-0284-4152-b760-423d6f91ebef/dqc_reference/checkm_data
[2023-03-16 02:38:44,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:44,839] [INFO] Task started: CheckM
[2023-03-16 02:38:44,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12982/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12982/checkm_input OceanDNA-b12982/checkm_result
[2023-03-16 02:39:28,761] [INFO] Task succeeded: CheckM
[2023-03-16 02:39:28,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:39:28,763] [INFO] ===== Completeness check finished =====
[2023-03-16 02:39:28,764] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:39:28,764] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12982/markers.fasta)
[2023-03-16 02:39:28,764] [INFO] Task started: Blastn
[2023-03-16 02:39:28,764] [INFO] Running command: blastn -query OceanDNA-b12982/markers.fasta -db /var/lib/cwl/stgee712094-0284-4152-b760-423d6f91ebef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12982/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:39:29,472] [INFO] Task succeeded: Blastn
[2023-03-16 02:39:29,473] [INFO] Selected 27 target genomes.
[2023-03-16 02:39:29,473] [INFO] Target genome list was writen to OceanDNA-b12982/target_genomes_gtdb.txt
[2023-03-16 02:39:30,109] [INFO] Task started: fastANI
[2023-03-16 02:39:30,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg234e89d2-4248-40d8-896d-be98d2212694/OceanDNA-b12982.fa --refList OceanDNA-b12982/target_genomes_gtdb.txt --output OceanDNA-b12982/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:39:45,802] [INFO] Task succeeded: fastANI
[2023-03-16 02:39:45,804] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 02:39:45,804] [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
GCA_003045995.1	s__Sam29DG08-bin30 sp003045995	98.47	488	536	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Sam29DG08-bin30	95.0	99.24	99.24	0.91	0.91	2	conclusive
--------------------------------------------------------------------------------
[2023-03-16 02:39:45,804] [INFO] GTDB search result was written to OceanDNA-b12982/result_gtdb.tsv
[2023-03-16 02:39:45,804] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:39:45,805] [INFO] DFAST_QC result json was written to OceanDNA-b12982/dqc_result.json
[2023-03-16 02:39:45,805] [INFO] DFAST_QC completed!
[2023-03-16 02:39:45,805] [INFO] Total running time: 0h1m41s