[2023-03-16 00:59:57,174] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:59:57,174] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:59:57,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg4633487c-9def-4016-ac85-a21f1808fd4b/dqc_reference
[2023-03-16 00:59:59,434] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:59:59,447] [INFO] Task started: Prodigal
[2023-03-16 00:59:59,447] [INFO] Running command: cat /var/lib/cwl/stg710c64d4-8f61-405d-8c5d-9e8e652c5f99/OceanDNA-b21895.fa | prodigal -d OceanDNA-b21895/cds.fna -a OceanDNA-b21895/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:00:04,161] [INFO] Task succeeded: Prodigal
[2023-03-16 01:00:04,162] [INFO] Task started: HMMsearch
[2023-03-16 01:00:04,162] [INFO] Running command: hmmsearch --tblout OceanDNA-b21895/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4633487c-9def-4016-ac85-a21f1808fd4b/dqc_reference/reference_markers.hmm OceanDNA-b21895/protein.faa > /dev/null
[2023-03-16 01:00:04,371] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:00:04,371] [INFO] Found 6/6 markers.
[2023-03-16 01:00:04,376] [INFO] Query marker FASTA was written to OceanDNA-b21895/markers.fasta
[2023-03-16 01:00:04,383] [INFO] Task started: Blastn
[2023-03-16 01:00:04,383] [INFO] Running command: blastn -query OceanDNA-b21895/markers.fasta -db /var/lib/cwl/stg4633487c-9def-4016-ac85-a21f1808fd4b/dqc_reference/reference_markers.fasta -out OceanDNA-b21895/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:00:06,512] [INFO] Task succeeded: Blastn
[2023-03-16 01:00:06,512] [INFO] Selected 10 target genomes.
[2023-03-16 01:00:06,513] [INFO] Target genome list was writen to OceanDNA-b21895/target_genomes.txt
[2023-03-16 01:00:06,543] [INFO] Task started: fastANI
[2023-03-16 01:00:06,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg710c64d4-8f61-405d-8c5d-9e8e652c5f99/OceanDNA-b21895.fa --refList OceanDNA-b21895/target_genomes.txt --output OceanDNA-b21895/fastani_result.tsv --threads 1
[2023-03-16 01:00:12,419] [INFO] Task succeeded: fastANI
[2023-03-16 01:00:12,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4633487c-9def-4016-ac85-a21f1808fd4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:00:12,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4633487c-9def-4016-ac85-a21f1808fd4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:00:12,420] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:00:12,420] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:00:12,420] [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 01:00:12,420] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21895/tc_result.tsv
[2023-03-16 01:00:12,420] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:00:12,421] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:00:12,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4633487c-9def-4016-ac85-a21f1808fd4b/dqc_reference/checkm_data
[2023-03-16 01:00:12,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:00:12,626] [INFO] Task started: CheckM
[2023-03-16 01:00:12,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21895/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21895/checkm_input OceanDNA-b21895/checkm_result
[2023-03-16 01:00:36,915] [INFO] Task succeeded: CheckM
[2023-03-16 01:00:36,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:00:36,916] [INFO] ===== Completeness check finished =====
[2023-03-16 01:00:36,916] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:00:36,917] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21895/markers.fasta)
[2023-03-16 01:00:36,919] [INFO] Task started: Blastn
[2023-03-16 01:00:36,919] [INFO] Running command: blastn -query OceanDNA-b21895/markers.fasta -db /var/lib/cwl/stg4633487c-9def-4016-ac85-a21f1808fd4b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21895/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:00:38,265] [INFO] Task succeeded: Blastn
[2023-03-16 01:00:38,266] [INFO] Selected 15 target genomes.
[2023-03-16 01:00:38,266] [INFO] Target genome list was writen to OceanDNA-b21895/target_genomes_gtdb.txt
[2023-03-16 01:00:38,330] [INFO] Task started: fastANI
[2023-03-16 01:00:38,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg710c64d4-8f61-405d-8c5d-9e8e652c5f99/OceanDNA-b21895.fa --refList OceanDNA-b21895/target_genomes_gtdb.txt --output OceanDNA-b21895/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:00:43,934] [INFO] Task succeeded: fastANI
[2023-03-16 01:00:43,936] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 01:00:43,936] [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_002331495.1	s__UBA2100 sp002331495	99.7025	159	189	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA2100;g__UBA2100	95.0	99.92	99.91	0.97	0.96	3	conclusive
--------------------------------------------------------------------------------
[2023-03-16 01:00:43,936] [INFO] GTDB search result was written to OceanDNA-b21895/result_gtdb.tsv
[2023-03-16 01:00:43,936] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:00:43,937] [INFO] DFAST_QC result json was written to OceanDNA-b21895/dqc_result.json
[2023-03-16 01:00:43,937] [INFO] DFAST_QC completed!
[2023-03-16 01:00:43,937] [INFO] Total running time: 0h0m47s