[2023-03-19 03:50:07,822] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,822] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,822] [INFO] DQC Reference Directory: /var/lib/cwl/stg52d30bb8-a0ac-4239-b5d0-13cbe3b87861/dqc_reference
[2023-03-19 03:50:09,580] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,581] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,581] [INFO] Running command: cat /var/lib/cwl/stgafbaac1a-3174-4be5-83d3-5b1d7e561185/OceanDNA-b44607.fa | prodigal -d OceanDNA-b44607/cds.fna -a OceanDNA-b44607/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:28,191] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:28,191] [INFO] Task started: HMMsearch
[2023-03-19 03:50:28,191] [INFO] Running command: hmmsearch --tblout OceanDNA-b44607/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52d30bb8-a0ac-4239-b5d0-13cbe3b87861/dqc_reference/reference_markers.hmm OceanDNA-b44607/protein.faa > /dev/null
[2023-03-19 03:50:28,387] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:28,388] [INFO] Found 6/6 markers.
[2023-03-19 03:50:28,409] [INFO] Query marker FASTA was written to OceanDNA-b44607/markers.fasta
[2023-03-19 03:50:28,409] [INFO] Task started: Blastn
[2023-03-19 03:50:28,409] [INFO] Running command: blastn -query OceanDNA-b44607/markers.fasta -db /var/lib/cwl/stg52d30bb8-a0ac-4239-b5d0-13cbe3b87861/dqc_reference/reference_markers.fasta -out OceanDNA-b44607/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:28,995] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:28,996] [INFO] Selected 29 target genomes.
[2023-03-19 03:50:28,996] [INFO] Target genome list was writen to OceanDNA-b44607/target_genomes.txt
[2023-03-19 03:50:29,009] [INFO] Task started: fastANI
[2023-03-19 03:50:29,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgafbaac1a-3174-4be5-83d3-5b1d7e561185/OceanDNA-b44607.fa --refList OceanDNA-b44607/target_genomes.txt --output OceanDNA-b44607/fastani_result.tsv --threads 1
[2023-03-19 03:50:45,942] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:45,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52d30bb8-a0ac-4239-b5d0-13cbe3b87861/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:45,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52d30bb8-a0ac-4239-b5d0-13cbe3b87861/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:45,943] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:45,943] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:50:45,943] [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
--------------------------------------------------------------------------------
[2023-03-19 03:50:45,987] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44607/tc_result.tsv
[2023-03-19 03:50:45,988] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:45,988] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:45,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52d30bb8-a0ac-4239-b5d0-13cbe3b87861/dqc_reference/checkm_data
[2023-03-19 03:50:45,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:46,010] [INFO] Task started: CheckM
[2023-03-19 03:50:46,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44607/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44607/checkm_input OceanDNA-b44607/checkm_result
[2023-03-19 03:51:33,911] [INFO] Task succeeded: CheckM
[2023-03-19 03:51:33,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:51:33,914] [INFO] ===== Completeness check finished =====
[2023-03-19 03:51:33,915] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:51:33,915] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44607/markers.fasta)
[2023-03-19 03:51:33,915] [INFO] Task started: Blastn
[2023-03-19 03:51:33,915] [INFO] Running command: blastn -query OceanDNA-b44607/markers.fasta -db /var/lib/cwl/stg52d30bb8-a0ac-4239-b5d0-13cbe3b87861/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44607/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:51:34,901] [INFO] Task succeeded: Blastn
[2023-03-19 03:51:34,902] [INFO] Selected 29 target genomes.
[2023-03-19 03:51:34,902] [INFO] Target genome list was writen to OceanDNA-b44607/target_genomes_gtdb.txt
[2023-03-19 03:51:34,940] [INFO] Task started: fastANI
[2023-03-19 03:51:34,940] [INFO] Running command: fastANI --query /var/lib/cwl/stgafbaac1a-3174-4be5-83d3-5b1d7e561185/OceanDNA-b44607.fa --refList OceanDNA-b44607/target_genomes_gtdb.txt --output OceanDNA-b44607/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:51:50,077] [INFO] Task succeeded: fastANI
[2023-03-19 03:51:50,080] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:51:50,080] [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_018701055.1	s__SZUA-117 sp018701055	95.7783	674	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SZUA-117	95.0	98.98	98.98	0.78	0.78	2	conclusive
GCA_905480255.1	s__SZUA-117 sp905480255	76.2206	57	1017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SZUA-117	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:51:50,080] [INFO] GTDB search result was written to OceanDNA-b44607/result_gtdb.tsv
[2023-03-19 03:51:50,080] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:51:50,081] [INFO] DFAST_QC result json was written to OceanDNA-b44607/dqc_result.json
[2023-03-19 03:51:50,081] [INFO] DFAST_QC completed!
[2023-03-19 03:51:50,081] [INFO] Total running time: 0h1m42s