[2023-03-14 12:33:23,817] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:33:23,817] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:33:23,817] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d9f9833-a44b-4cec-9b20-9f7c5045f9d0/dqc_reference
[2023-03-14 12:33:25,017] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:33:25,017] [INFO] Task started: Prodigal
[2023-03-14 12:33:25,017] [INFO] Running command: cat /var/lib/cwl/stgcc50a2e0-6397-4081-a1fa-62dc000dcf78/OceanDNA-b21719.fa | prodigal -d OceanDNA-b21719/cds.fna -a OceanDNA-b21719/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:33:27,517] [INFO] Task succeeded: Prodigal
[2023-03-14 12:33:27,517] [INFO] Task started: HMMsearch
[2023-03-14 12:33:27,517] [INFO] Running command: hmmsearch --tblout OceanDNA-b21719/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d9f9833-a44b-4cec-9b20-9f7c5045f9d0/dqc_reference/reference_markers.hmm OceanDNA-b21719/protein.faa > /dev/null
[2023-03-14 12:33:27,636] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:33:27,636] [INFO] Found 6/6 markers.
[2023-03-14 12:33:27,642] [INFO] Query marker FASTA was written to OceanDNA-b21719/markers.fasta
[2023-03-14 12:33:27,644] [INFO] Task started: Blastn
[2023-03-14 12:33:27,644] [INFO] Running command: blastn -query OceanDNA-b21719/markers.fasta -db /var/lib/cwl/stg5d9f9833-a44b-4cec-9b20-9f7c5045f9d0/dqc_reference/reference_markers.fasta -out OceanDNA-b21719/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:33:28,190] [INFO] Task succeeded: Blastn
[2023-03-14 12:33:28,191] [INFO] Selected 15 target genomes.
[2023-03-14 12:33:28,192] [INFO] Target genome list was writen to OceanDNA-b21719/target_genomes.txt
[2023-03-14 12:33:28,202] [INFO] Task started: fastANI
[2023-03-14 12:33:28,202] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc50a2e0-6397-4081-a1fa-62dc000dcf78/OceanDNA-b21719.fa --refList OceanDNA-b21719/target_genomes.txt --output OceanDNA-b21719/fastani_result.tsv --threads 1
[2023-03-14 12:33:34,705] [INFO] Task succeeded: fastANI
[2023-03-14 12:33:34,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d9f9833-a44b-4cec-9b20-9f7c5045f9d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:33:34,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d9f9833-a44b-4cec-9b20-9f7c5045f9d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:33:34,706] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:33:34,706] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:33:34,706] [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
--------------------------------------------------------------------------------
[2023-03-14 12:33:34,706] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21719/tc_result.tsv
[2023-03-14 12:33:34,706] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:33:34,707] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:33:34,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d9f9833-a44b-4cec-9b20-9f7c5045f9d0/dqc_reference/checkm_data
[2023-03-14 12:33:34,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:33:34,719] [INFO] Task started: CheckM
[2023-03-14 12:33:34,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21719/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21719/checkm_input OceanDNA-b21719/checkm_result
[2023-03-14 12:33:47,938] [INFO] Task succeeded: CheckM
[2023-03-14 12:33:47,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:33:47,941] [INFO] ===== Completeness check finished =====
[2023-03-14 12:33:47,941] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:33:47,941] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21719/markers.fasta)
[2023-03-14 12:33:47,943] [INFO] Task started: Blastn
[2023-03-14 12:33:47,943] [INFO] Running command: blastn -query OceanDNA-b21719/markers.fasta -db /var/lib/cwl/stg5d9f9833-a44b-4cec-9b20-9f7c5045f9d0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21719/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:33:48,783] [INFO] Task succeeded: Blastn
[2023-03-14 12:33:48,783] [INFO] Selected 15 target genomes.
[2023-03-14 12:33:48,783] [INFO] Target genome list was writen to OceanDNA-b21719/target_genomes_gtdb.txt
[2023-03-14 12:33:48,797] [INFO] Task started: fastANI
[2023-03-14 12:33:48,797] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc50a2e0-6397-4081-a1fa-62dc000dcf78/OceanDNA-b21719.fa --refList OceanDNA-b21719/target_genomes_gtdb.txt --output OceanDNA-b21719/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:33:54,237] [INFO] Task succeeded: fastANI
[2023-03-14 12:33:54,238] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:33:54,239] [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_003539915.1	s__UBA11618 sp003539915	94.5414	80	130	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA6257;f__UBA11618;g__UBA11618	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:33:54,240] [INFO] GTDB search result was written to OceanDNA-b21719/result_gtdb.tsv
[2023-03-14 12:33:54,240] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:33:54,241] [INFO] DFAST_QC result json was written to OceanDNA-b21719/dqc_result.json
[2023-03-14 12:33:54,241] [INFO] DFAST_QC completed!
[2023-03-14 12:33:54,241] [INFO] Total running time: 0h0m30s