[2023-03-14 13:09:10,234] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:09:10,234] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:09:10,234] [INFO] DQC Reference Directory: /var/lib/cwl/stga057d120-d0ac-4a14-99e6-a2f93f12b368/dqc_reference
[2023-03-14 13:09:11,446] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:09:11,446] [INFO] Task started: Prodigal
[2023-03-14 13:09:11,446] [INFO] Running command: cat /var/lib/cwl/stg49029812-258f-4ed9-8614-c73f977d838a/OceanDNA-b15112.fa | prodigal -d OceanDNA-b15112/cds.fna -a OceanDNA-b15112/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:09:22,511] [INFO] Task succeeded: Prodigal
[2023-03-14 13:09:22,512] [INFO] Task started: HMMsearch
[2023-03-14 13:09:22,512] [INFO] Running command: hmmsearch --tblout OceanDNA-b15112/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga057d120-d0ac-4a14-99e6-a2f93f12b368/dqc_reference/reference_markers.hmm OceanDNA-b15112/protein.faa > /dev/null
[2023-03-14 13:09:22,826] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:09:22,827] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg49029812-258f-4ed9-8614-c73f977d838a/OceanDNA-b15112.fa]
[2023-03-14 13:09:22,848] [INFO] Query marker FASTA was written to OceanDNA-b15112/markers.fasta
[2023-03-14 13:09:22,854] [INFO] Task started: Blastn
[2023-03-14 13:09:22,854] [INFO] Running command: blastn -query OceanDNA-b15112/markers.fasta -db /var/lib/cwl/stga057d120-d0ac-4a14-99e6-a2f93f12b368/dqc_reference/reference_markers.fasta -out OceanDNA-b15112/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:09:23,352] [INFO] Task succeeded: Blastn
[2023-03-14 13:09:23,354] [INFO] Selected 5 target genomes.
[2023-03-14 13:09:23,354] [INFO] Target genome list was writen to OceanDNA-b15112/target_genomes.txt
[2023-03-14 13:09:23,357] [INFO] Task started: fastANI
[2023-03-14 13:09:23,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg49029812-258f-4ed9-8614-c73f977d838a/OceanDNA-b15112.fa --refList OceanDNA-b15112/target_genomes.txt --output OceanDNA-b15112/fastani_result.tsv --threads 1
[2023-03-14 13:09:27,559] [INFO] Task succeeded: fastANI
[2023-03-14 13:09:27,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga057d120-d0ac-4a14-99e6-a2f93f12b368/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:09:27,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga057d120-d0ac-4a14-99e6-a2f93f12b368/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:09:27,560] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:09:27,560] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:09:27,560] [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 13:09:27,561] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15112/tc_result.tsv
[2023-03-14 13:09:27,561] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:09:27,561] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:09:27,561] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga057d120-d0ac-4a14-99e6-a2f93f12b368/dqc_reference/checkm_data
[2023-03-14 13:09:27,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:09:27,625] [INFO] Task started: CheckM
[2023-03-14 13:09:27,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15112/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15112/checkm_input OceanDNA-b15112/checkm_result
[2023-03-14 13:10:02,521] [INFO] Task succeeded: CheckM
[2023-03-14 13:10:02,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.30%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:10:02,525] [INFO] ===== Completeness check finished =====
[2023-03-14 13:10:02,525] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:10:02,525] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15112/markers.fasta)
[2023-03-14 13:10:02,528] [INFO] Task started: Blastn
[2023-03-14 13:10:02,528] [INFO] Running command: blastn -query OceanDNA-b15112/markers.fasta -db /var/lib/cwl/stga057d120-d0ac-4a14-99e6-a2f93f12b368/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15112/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:10:03,184] [INFO] Task succeeded: Blastn
[2023-03-14 13:10:03,186] [INFO] Selected 10 target genomes.
[2023-03-14 13:10:03,186] [INFO] Target genome list was writen to OceanDNA-b15112/target_genomes_gtdb.txt
[2023-03-14 13:10:03,202] [INFO] Task started: fastANI
[2023-03-14 13:10:03,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg49029812-258f-4ed9-8614-c73f977d838a/OceanDNA-b15112.fa --refList OceanDNA-b15112/target_genomes_gtdb.txt --output OceanDNA-b15112/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:10:08,774] [INFO] Task succeeded: fastANI
[2023-03-14 13:10:08,777] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:10:08,777] [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_002311865.1	s__UBA1151 sp002311865	85.7568	337	376	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__UBA1151	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204555.1	s__UBA1151 sp013204555	77.9866	189	376	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__UBA1151	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:10:08,778] [INFO] GTDB search result was written to OceanDNA-b15112/result_gtdb.tsv
[2023-03-14 13:10:08,778] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:10:08,779] [INFO] DFAST_QC result json was written to OceanDNA-b15112/dqc_result.json
[2023-03-14 13:10:08,779] [INFO] DFAST_QC completed!
[2023-03-14 13:10:08,779] [INFO] Total running time: 0h0m59s