[2023-03-17 10:19:15,245] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:19:15,246] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:19:15,246] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ac6fbbb-0fbc-4490-b341-d7b6dd5cefe2/dqc_reference
[2023-03-17 10:19:17,001] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:19:17,001] [INFO] Task started: Prodigal
[2023-03-17 10:19:17,001] [INFO] Running command: cat /var/lib/cwl/stg515766cc-557b-4b0a-97c3-6617fff5cf32/OceanDNA-b30842.fa | prodigal -d OceanDNA-b30842/cds.fna -a OceanDNA-b30842/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:19:26,935] [INFO] Task succeeded: Prodigal
[2023-03-17 10:19:26,935] [INFO] Task started: HMMsearch
[2023-03-17 10:19:26,935] [INFO] Running command: hmmsearch --tblout OceanDNA-b30842/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ac6fbbb-0fbc-4490-b341-d7b6dd5cefe2/dqc_reference/reference_markers.hmm OceanDNA-b30842/protein.faa > /dev/null
[2023-03-17 10:19:27,101] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:19:27,102] [INFO] Found 6/6 markers.
[2023-03-17 10:19:27,121] [INFO] Query marker FASTA was written to OceanDNA-b30842/markers.fasta
[2023-03-17 10:19:27,122] [INFO] Task started: Blastn
[2023-03-17 10:19:27,122] [INFO] Running command: blastn -query OceanDNA-b30842/markers.fasta -db /var/lib/cwl/stg9ac6fbbb-0fbc-4490-b341-d7b6dd5cefe2/dqc_reference/reference_markers.fasta -out OceanDNA-b30842/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:19:27,626] [INFO] Task succeeded: Blastn
[2023-03-17 10:19:27,628] [INFO] Selected 10 target genomes.
[2023-03-17 10:19:27,629] [INFO] Target genome list was writen to OceanDNA-b30842/target_genomes.txt
[2023-03-17 10:19:27,635] [INFO] Task started: fastANI
[2023-03-17 10:19:27,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg515766cc-557b-4b0a-97c3-6617fff5cf32/OceanDNA-b30842.fa --refList OceanDNA-b30842/target_genomes.txt --output OceanDNA-b30842/fastani_result.tsv --threads 1
[2023-03-17 10:19:33,492] [INFO] Task succeeded: fastANI
[2023-03-17 10:19:33,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ac6fbbb-0fbc-4490-b341-d7b6dd5cefe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:19:33,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ac6fbbb-0fbc-4490-b341-d7b6dd5cefe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:19:33,493] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:19:33,493] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:19:33,493] [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
--------------------------------------------------------------------------------
[2023-03-17 10:19:33,495] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30842/tc_result.tsv
[2023-03-17 10:19:33,497] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:19:33,497] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:19:33,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ac6fbbb-0fbc-4490-b341-d7b6dd5cefe2/dqc_reference/checkm_data
[2023-03-17 10:19:33,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:19:33,515] [INFO] Task started: CheckM
[2023-03-17 10:19:33,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30842/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30842/checkm_input OceanDNA-b30842/checkm_result
[2023-03-17 10:20:02,873] [INFO] Task succeeded: CheckM
[2023-03-17 10:20:02,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.57%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:20:02,969] [INFO] ===== Completeness check finished =====
[2023-03-17 10:20:02,969] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:20:02,969] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30842/markers.fasta)
[2023-03-17 10:20:02,971] [INFO] Task started: Blastn
[2023-03-17 10:20:02,971] [INFO] Running command: blastn -query OceanDNA-b30842/markers.fasta -db /var/lib/cwl/stg9ac6fbbb-0fbc-4490-b341-d7b6dd5cefe2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30842/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:20:03,674] [INFO] Task succeeded: Blastn
[2023-03-17 10:20:03,678] [INFO] Selected 20 target genomes.
[2023-03-17 10:20:03,678] [INFO] Target genome list was writen to OceanDNA-b30842/target_genomes_gtdb.txt
[2023-03-17 10:20:04,279] [INFO] Task started: fastANI
[2023-03-17 10:20:04,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg515766cc-557b-4b0a-97c3-6617fff5cf32/OceanDNA-b30842.fa --refList OceanDNA-b30842/target_genomes_gtdb.txt --output OceanDNA-b30842/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:20:10,355] [INFO] Task succeeded: fastANI
[2023-03-17 10:20:10,357] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:20:10,357] [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_002722175.1	s__GCA-2722175 sp002722175	99.7125	534	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__GCA-2722175	95.0	99.84	99.84	0.90	0.90	2	conclusive
--------------------------------------------------------------------------------
[2023-03-17 10:20:10,361] [INFO] GTDB search result was written to OceanDNA-b30842/result_gtdb.tsv
[2023-03-17 10:20:10,366] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:20:10,369] [INFO] DFAST_QC result json was written to OceanDNA-b30842/dqc_result.json
[2023-03-17 10:20:10,370] [INFO] DFAST_QC completed!
[2023-03-17 10:20:10,370] [INFO] Total running time: 0h0m55s