[2023-03-16 21:45:13,532] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:13,532] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:13,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg33e13e56-fd34-445e-89c1-a3384f07f1ce/dqc_reference
[2023-03-16 21:45:15,331] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:15,331] [INFO] Task started: Prodigal
[2023-03-16 21:45:15,332] [INFO] Running command: cat /var/lib/cwl/stg278f1401-83c9-459c-a973-aa58d54bffbb/OceanDNA-b20645.fa | prodigal -d OceanDNA-b20645/cds.fna -a OceanDNA-b20645/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:18,527] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:18,528] [INFO] Task started: HMMsearch
[2023-03-16 21:45:18,528] [INFO] Running command: hmmsearch --tblout OceanDNA-b20645/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33e13e56-fd34-445e-89c1-a3384f07f1ce/dqc_reference/reference_markers.hmm OceanDNA-b20645/protein.faa > /dev/null
[2023-03-16 21:45:18,731] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:18,732] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg278f1401-83c9-459c-a973-aa58d54bffbb/OceanDNA-b20645.fa]
[2023-03-16 21:45:18,740] [INFO] Query marker FASTA was written to OceanDNA-b20645/markers.fasta
[2023-03-16 21:45:18,741] [INFO] Task started: Blastn
[2023-03-16 21:45:18,741] [INFO] Running command: blastn -query OceanDNA-b20645/markers.fasta -db /var/lib/cwl/stg33e13e56-fd34-445e-89c1-a3384f07f1ce/dqc_reference/reference_markers.fasta -out OceanDNA-b20645/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:21,766] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:21,767] [INFO] Selected 16 target genomes.
[2023-03-16 21:45:21,767] [INFO] Target genome list was writen to OceanDNA-b20645/target_genomes.txt
[2023-03-16 21:45:21,781] [INFO] Task started: fastANI
[2023-03-16 21:45:21,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg278f1401-83c9-459c-a973-aa58d54bffbb/OceanDNA-b20645.fa --refList OceanDNA-b20645/target_genomes.txt --output OceanDNA-b20645/fastani_result.tsv --threads 1
[2023-03-16 21:45:29,967] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:29,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33e13e56-fd34-445e-89c1-a3384f07f1ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:29,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33e13e56-fd34-445e-89c1-a3384f07f1ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:29,968] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:29,968] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 21:45:29,968] [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 21:45:29,968] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20645/tc_result.tsv
[2023-03-16 21:45:29,968] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:29,968] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:29,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33e13e56-fd34-445e-89c1-a3384f07f1ce/dqc_reference/checkm_data
[2023-03-16 21:45:29,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:29,973] [INFO] Task started: CheckM
[2023-03-16 21:45:29,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20645/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20645/checkm_input OceanDNA-b20645/checkm_result
[2023-03-16 21:45:44,819] [INFO] Task succeeded: CheckM
[2023-03-16 21:45:44,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:45:44,821] [INFO] ===== Completeness check finished =====
[2023-03-16 21:45:44,821] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:45:44,821] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20645/markers.fasta)
[2023-03-16 21:45:44,821] [INFO] Task started: Blastn
[2023-03-16 21:45:44,821] [INFO] Running command: blastn -query OceanDNA-b20645/markers.fasta -db /var/lib/cwl/stg33e13e56-fd34-445e-89c1-a3384f07f1ce/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20645/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:45,560] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:45,561] [INFO] Selected 17 target genomes.
[2023-03-16 21:45:45,562] [INFO] Target genome list was writen to OceanDNA-b20645/target_genomes_gtdb.txt
[2023-03-16 21:45:45,600] [INFO] Task started: fastANI
[2023-03-16 21:45:45,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg278f1401-83c9-459c-a973-aa58d54bffbb/OceanDNA-b20645.fa --refList OceanDNA-b20645/target_genomes_gtdb.txt --output OceanDNA-b20645/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:45:53,184] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:53,186] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:45:53,186] [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_018671635.1	s__JABHHG01 sp018671635	82.1977	113	157	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__D37C17;g__JABHHG01	95.0	99.09	99.01	0.82	0.76	4	-
--------------------------------------------------------------------------------
[2023-03-16 21:45:53,187] [INFO] GTDB search result was written to OceanDNA-b20645/result_gtdb.tsv
[2023-03-16 21:45:53,187] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:45:53,187] [INFO] DFAST_QC result json was written to OceanDNA-b20645/dqc_result.json
[2023-03-16 21:45:53,187] [INFO] DFAST_QC completed!
[2023-03-16 21:45:53,187] [INFO] Total running time: 0h0m40s