[2023-03-19 03:36:54,111] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:36:54,112] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:36:54,112] [INFO] DQC Reference Directory: /var/lib/cwl/stg8337c10c-f746-4795-a3bb-40bf7a6e854f/dqc_reference
[2023-03-19 03:36:55,287] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:36:55,288] [INFO] Task started: Prodigal
[2023-03-19 03:36:55,288] [INFO] Running command: cat /var/lib/cwl/stgab1c9e21-087e-4095-b210-ed1d9dc9c6f8/OceanDNA-b15330.fa | prodigal -d OceanDNA-b15330/cds.fna -a OceanDNA-b15330/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:37:00,359] [INFO] Task succeeded: Prodigal
[2023-03-19 03:37:00,360] [INFO] Task started: HMMsearch
[2023-03-19 03:37:00,360] [INFO] Running command: hmmsearch --tblout OceanDNA-b15330/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8337c10c-f746-4795-a3bb-40bf7a6e854f/dqc_reference/reference_markers.hmm OceanDNA-b15330/protein.faa > /dev/null
[2023-03-19 03:37:00,503] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:37:00,504] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgab1c9e21-087e-4095-b210-ed1d9dc9c6f8/OceanDNA-b15330.fa]
[2023-03-19 03:37:00,515] [INFO] Query marker FASTA was written to OceanDNA-b15330/markers.fasta
[2023-03-19 03:37:00,516] [INFO] Task started: Blastn
[2023-03-19 03:37:00,516] [INFO] Running command: blastn -query OceanDNA-b15330/markers.fasta -db /var/lib/cwl/stg8337c10c-f746-4795-a3bb-40bf7a6e854f/dqc_reference/reference_markers.fasta -out OceanDNA-b15330/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:37:00,996] [INFO] Task succeeded: Blastn
[2023-03-19 03:37:00,997] [INFO] Selected 12 target genomes.
[2023-03-19 03:37:00,997] [INFO] Target genome list was writen to OceanDNA-b15330/target_genomes.txt
[2023-03-19 03:37:01,004] [INFO] Task started: fastANI
[2023-03-19 03:37:01,005] [INFO] Running command: fastANI --query /var/lib/cwl/stgab1c9e21-087e-4095-b210-ed1d9dc9c6f8/OceanDNA-b15330.fa --refList OceanDNA-b15330/target_genomes.txt --output OceanDNA-b15330/fastani_result.tsv --threads 1
[2023-03-19 03:37:06,033] [INFO] Task succeeded: fastANI
[2023-03-19 03:37:06,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8337c10c-f746-4795-a3bb-40bf7a6e854f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:37:06,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8337c10c-f746-4795-a3bb-40bf7a6e854f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:37:06,033] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:37:06,033] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:37:06,033] [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 03:37:06,034] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15330/tc_result.tsv
[2023-03-19 03:37:06,035] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:37:06,035] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:37:06,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8337c10c-f746-4795-a3bb-40bf7a6e854f/dqc_reference/checkm_data
[2023-03-19 03:37:06,038] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:37:06,514] [INFO] Task started: CheckM
[2023-03-19 03:37:06,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15330/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15330/checkm_input OceanDNA-b15330/checkm_result
[2023-03-19 03:37:25,350] [INFO] Task succeeded: CheckM
[2023-03-19 03:37:25,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.99%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:37:25,353] [INFO] ===== Completeness check finished =====
[2023-03-19 03:37:25,353] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:37:25,353] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15330/markers.fasta)
[2023-03-19 03:37:25,353] [INFO] Task started: Blastn
[2023-03-19 03:37:25,353] [INFO] Running command: blastn -query OceanDNA-b15330/markers.fasta -db /var/lib/cwl/stg8337c10c-f746-4795-a3bb-40bf7a6e854f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15330/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:37:25,955] [INFO] Task succeeded: Blastn
[2023-03-19 03:37:25,957] [INFO] Selected 15 target genomes.
[2023-03-19 03:37:25,957] [INFO] Target genome list was writen to OceanDNA-b15330/target_genomes_gtdb.txt
[2023-03-19 03:37:25,971] [INFO] Task started: fastANI
[2023-03-19 03:37:25,972] [INFO] Running command: fastANI --query /var/lib/cwl/stgab1c9e21-087e-4095-b210-ed1d9dc9c6f8/OceanDNA-b15330.fa --refList OceanDNA-b15330/target_genomes_gtdb.txt --output OceanDNA-b15330/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:37:32,539] [INFO] Task succeeded: fastANI
[2023-03-19 03:37:32,542] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:37:32,542] [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_002712585.1	s__GCA-2712585 sp002712585	94.6665	244	298	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__GCA-2712585;g__GCA-2712585	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:37:32,543] [INFO] GTDB search result was written to OceanDNA-b15330/result_gtdb.tsv
[2023-03-19 03:37:32,543] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:37:32,544] [INFO] DFAST_QC result json was written to OceanDNA-b15330/dqc_result.json
[2023-03-19 03:37:32,544] [INFO] DFAST_QC completed!
[2023-03-19 03:37:32,545] [INFO] Total running time: 0h0m38s