[2023-03-16 08:50:59,882] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:50:59,884] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:50:59,884] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd29be80-49fc-4f00-ad81-209b8e2eb409/dqc_reference
[2023-03-16 08:51:01,124] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:51:01,125] [INFO] Task started: Prodigal
[2023-03-16 08:51:01,125] [INFO] Running command: cat /var/lib/cwl/stg113dc392-2160-4d57-b851-5b7c8bd992d8/OceanDNA-b41322.fa | prodigal -d OceanDNA-b41322/cds.fna -a OceanDNA-b41322/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:51:09,360] [INFO] Task succeeded: Prodigal
[2023-03-16 08:51:09,360] [INFO] Task started: HMMsearch
[2023-03-16 08:51:09,360] [INFO] Running command: hmmsearch --tblout OceanDNA-b41322/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd29be80-49fc-4f00-ad81-209b8e2eb409/dqc_reference/reference_markers.hmm OceanDNA-b41322/protein.faa > /dev/null
[2023-03-16 08:51:09,556] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:51:09,557] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg113dc392-2160-4d57-b851-5b7c8bd992d8/OceanDNA-b41322.fa]
[2023-03-16 08:51:09,584] [INFO] Query marker FASTA was written to OceanDNA-b41322/markers.fasta
[2023-03-16 08:51:09,584] [INFO] Task started: Blastn
[2023-03-16 08:51:09,584] [INFO] Running command: blastn -query OceanDNA-b41322/markers.fasta -db /var/lib/cwl/stgfd29be80-49fc-4f00-ad81-209b8e2eb409/dqc_reference/reference_markers.fasta -out OceanDNA-b41322/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:10,035] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:10,043] [INFO] Selected 30 target genomes.
[2023-03-16 08:51:10,044] [INFO] Target genome list was writen to OceanDNA-b41322/target_genomes.txt
[2023-03-16 08:51:10,064] [INFO] Task started: fastANI
[2023-03-16 08:51:10,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg113dc392-2160-4d57-b851-5b7c8bd992d8/OceanDNA-b41322.fa --refList OceanDNA-b41322/target_genomes.txt --output OceanDNA-b41322/fastani_result.tsv --threads 1
[2023-03-16 08:51:26,814] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:26,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd29be80-49fc-4f00-ad81-209b8e2eb409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:51:26,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd29be80-49fc-4f00-ad81-209b8e2eb409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:51:26,815] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:51:26,815] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:51:26,815] [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 08:51:26,816] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41322/tc_result.tsv
[2023-03-16 08:51:26,818] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:51:26,818] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:51:26,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd29be80-49fc-4f00-ad81-209b8e2eb409/dqc_reference/checkm_data
[2023-03-16 08:51:26,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:51:26,826] [INFO] Task started: CheckM
[2023-03-16 08:51:26,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41322/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41322/checkm_input OceanDNA-b41322/checkm_result
[2023-03-16 08:51:53,801] [INFO] Task succeeded: CheckM
[2023-03-16 08:51:53,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.76%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 08:51:53,818] [INFO] ===== Completeness check finished =====
[2023-03-16 08:51:53,818] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:51:53,818] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41322/markers.fasta)
[2023-03-16 08:51:53,819] [INFO] Task started: Blastn
[2023-03-16 08:51:53,819] [INFO] Running command: blastn -query OceanDNA-b41322/markers.fasta -db /var/lib/cwl/stgfd29be80-49fc-4f00-ad81-209b8e2eb409/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41322/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:54,287] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:54,291] [INFO] Selected 28 target genomes.
[2023-03-16 08:51:54,291] [INFO] Target genome list was writen to OceanDNA-b41322/target_genomes_gtdb.txt
[2023-03-16 08:51:54,338] [INFO] Task started: fastANI
[2023-03-16 08:51:54,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg113dc392-2160-4d57-b851-5b7c8bd992d8/OceanDNA-b41322.fa --refList OceanDNA-b41322/target_genomes_gtdb.txt --output OceanDNA-b41322/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:52:14,112] [INFO] Task succeeded: fastANI
[2023-03-16 08:52:14,115] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:52:14,115] [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_002162985.1	s__Bermanella sp002162985	84.8545	86	187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:52:14,117] [INFO] GTDB search result was written to OceanDNA-b41322/result_gtdb.tsv
[2023-03-16 08:52:14,119] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:52:14,122] [INFO] DFAST_QC result json was written to OceanDNA-b41322/dqc_result.json
[2023-03-16 08:52:14,122] [INFO] DFAST_QC completed!
[2023-03-16 08:52:14,122] [INFO] Total running time: 0h1m14s