[2023-03-14 11:17:27,803] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:17:27,803] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:17:27,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg13a35937-e720-48aa-9675-1c7227064bec/dqc_reference
[2023-03-14 11:17:28,893] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:17:28,893] [INFO] Task started: Prodigal
[2023-03-14 11:17:28,893] [INFO] Running command: cat /var/lib/cwl/stg1f896580-9fa5-4970-a223-1d9acd816534/OceanDNA-b34785.fa | prodigal -d OceanDNA-b34785/cds.fna -a OceanDNA-b34785/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:17:45,990] [INFO] Task succeeded: Prodigal
[2023-03-14 11:17:45,990] [INFO] Task started: HMMsearch
[2023-03-14 11:17:45,990] [INFO] Running command: hmmsearch --tblout OceanDNA-b34785/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13a35937-e720-48aa-9675-1c7227064bec/dqc_reference/reference_markers.hmm OceanDNA-b34785/protein.faa > /dev/null
[2023-03-14 11:17:46,200] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:17:46,201] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1f896580-9fa5-4970-a223-1d9acd816534/OceanDNA-b34785.fa]
[2023-03-14 11:17:46,223] [INFO] Query marker FASTA was written to OceanDNA-b34785/markers.fasta
[2023-03-14 11:17:46,223] [INFO] Task started: Blastn
[2023-03-14 11:17:46,223] [INFO] Running command: blastn -query OceanDNA-b34785/markers.fasta -db /var/lib/cwl/stg13a35937-e720-48aa-9675-1c7227064bec/dqc_reference/reference_markers.fasta -out OceanDNA-b34785/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:17:46,747] [INFO] Task succeeded: Blastn
[2023-03-14 11:17:46,749] [INFO] Selected 31 target genomes.
[2023-03-14 11:17:46,749] [INFO] Target genome list was writen to OceanDNA-b34785/target_genomes.txt
[2023-03-14 11:17:46,769] [INFO] Task started: fastANI
[2023-03-14 11:17:46,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f896580-9fa5-4970-a223-1d9acd816534/OceanDNA-b34785.fa --refList OceanDNA-b34785/target_genomes.txt --output OceanDNA-b34785/fastani_result.tsv --threads 1
[2023-03-14 11:18:07,127] [INFO] Task succeeded: fastANI
[2023-03-14 11:18:07,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13a35937-e720-48aa-9675-1c7227064bec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:18:07,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13a35937-e720-48aa-9675-1c7227064bec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:18:07,127] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:18:07,127] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:18:07,128] [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 11:18:07,129] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34785/tc_result.tsv
[2023-03-14 11:18:07,130] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:18:07,130] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:18:07,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13a35937-e720-48aa-9675-1c7227064bec/dqc_reference/checkm_data
[2023-03-14 11:18:07,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:18:07,138] [INFO] Task started: CheckM
[2023-03-14 11:18:07,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34785/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34785/checkm_input OceanDNA-b34785/checkm_result
[2023-03-14 11:18:52,140] [INFO] Task succeeded: CheckM
[2023-03-14 11:18:52,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.88%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:18:52,143] [INFO] ===== Completeness check finished =====
[2023-03-14 11:18:52,144] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:18:52,144] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34785/markers.fasta)
[2023-03-14 11:18:52,145] [INFO] Task started: Blastn
[2023-03-14 11:18:52,145] [INFO] Running command: blastn -query OceanDNA-b34785/markers.fasta -db /var/lib/cwl/stg13a35937-e720-48aa-9675-1c7227064bec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34785/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:18:52,897] [INFO] Task succeeded: Blastn
[2023-03-14 11:18:52,899] [INFO] Selected 35 target genomes.
[2023-03-14 11:18:52,899] [INFO] Target genome list was writen to OceanDNA-b34785/target_genomes_gtdb.txt
[2023-03-14 11:18:52,991] [INFO] Task started: fastANI
[2023-03-14 11:18:52,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f896580-9fa5-4970-a223-1d9acd816534/OceanDNA-b34785.fa --refList OceanDNA-b34785/target_genomes_gtdb.txt --output OceanDNA-b34785/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:19:14,361] [INFO] Task succeeded: fastANI
[2023-03-14 11:19:14,363] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:19:14,363] [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
GCF_000252165.1	s__Glaciecola punicea	77.0611	124	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	99.53	99.53	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-14 11:19:14,364] [INFO] GTDB search result was written to OceanDNA-b34785/result_gtdb.tsv
[2023-03-14 11:19:14,364] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:19:14,365] [INFO] DFAST_QC result json was written to OceanDNA-b34785/dqc_result.json
[2023-03-14 11:19:14,365] [INFO] DFAST_QC completed!
[2023-03-14 11:19:14,365] [INFO] Total running time: 0h1m47s