[2023-03-15 17:46:31,638] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,638] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ec8cbec-0a25-4ae4-8cef-05f108c3d5dc/dqc_reference
[2023-03-15 17:46:32,784] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,784] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,784] [INFO] Running command: cat /var/lib/cwl/stgc086e0a7-f353-40b4-9c5c-fa9e6d3d2f8e/OceanDNA-a1354.fa | prodigal -d OceanDNA-a1354/cds.fna -a OceanDNA-a1354/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:40,513] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:40,513] [INFO] Task started: HMMsearch
[2023-03-15 17:46:40,513] [INFO] Running command: hmmsearch --tblout OceanDNA-a1354/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ec8cbec-0a25-4ae4-8cef-05f108c3d5dc/dqc_reference/reference_markers.hmm OceanDNA-a1354/protein.faa > /dev/null
[2023-03-15 17:46:40,763] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:40,763] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc086e0a7-f353-40b4-9c5c-fa9e6d3d2f8e/OceanDNA-a1354.fa]
[2023-03-15 17:46:40,780] [INFO] Query marker FASTA was written to OceanDNA-a1354/markers.fasta
[2023-03-15 17:46:40,781] [INFO] Task started: Blastn
[2023-03-15 17:46:40,781] [INFO] Running command: blastn -query OceanDNA-a1354/markers.fasta -db /var/lib/cwl/stg4ec8cbec-0a25-4ae4-8cef-05f108c3d5dc/dqc_reference/reference_markers.fasta -out OceanDNA-a1354/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:41,256] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:41,258] [INFO] Selected 5 target genomes.
[2023-03-15 17:46:41,258] [INFO] Target genome list was writen to OceanDNA-a1354/target_genomes.txt
[2023-03-15 17:46:41,261] [INFO] Task started: fastANI
[2023-03-15 17:46:41,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgc086e0a7-f353-40b4-9c5c-fa9e6d3d2f8e/OceanDNA-a1354.fa --refList OceanDNA-a1354/target_genomes.txt --output OceanDNA-a1354/fastani_result.tsv --threads 1
[2023-03-15 17:46:43,560] [INFO] Task succeeded: fastANI
[2023-03-15 17:46:43,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ec8cbec-0a25-4ae4-8cef-05f108c3d5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:46:43,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ec8cbec-0a25-4ae4-8cef-05f108c3d5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:46:43,561] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:46:43,561] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:46:43,561] [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
--------------------------------------------------------------------------------
[2023-03-15 17:46:43,562] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1354/tc_result.tsv
[2023-03-15 17:46:43,562] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:46:43,562] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:46:43,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ec8cbec-0a25-4ae4-8cef-05f108c3d5dc/dqc_reference/checkm_data
[2023-03-15 17:46:43,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:46:43,570] [INFO] Task started: CheckM
[2023-03-15 17:46:43,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1354/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1354/checkm_input OceanDNA-a1354/checkm_result
[2023-03-15 17:47:08,153] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:08,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:08,175] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:08,176] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:08,176] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1354/markers.fasta)
[2023-03-15 17:47:08,177] [INFO] Task started: Blastn
[2023-03-15 17:47:08,177] [INFO] Running command: blastn -query OceanDNA-a1354/markers.fasta -db /var/lib/cwl/stg4ec8cbec-0a25-4ae4-8cef-05f108c3d5dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1354/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:08,779] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:08,781] [INFO] Selected 8 target genomes.
[2023-03-15 17:47:08,781] [INFO] Target genome list was writen to OceanDNA-a1354/target_genomes_gtdb.txt
[2023-03-15 17:47:08,791] [INFO] Task started: fastANI
[2023-03-15 17:47:08,792] [INFO] Running command: fastANI --query /var/lib/cwl/stgc086e0a7-f353-40b4-9c5c-fa9e6d3d2f8e/OceanDNA-a1354.fa --refList OceanDNA-a1354/target_genomes_gtdb.txt --output OceanDNA-a1354/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:47:11,193] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:11,196] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:47:11,196] [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_018661705.1	s__JABHXF01 sp018661705	99.9469	454	497	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__DSVV01;g__JABHXF01	95.0	99.97	99.96	0.96	0.94	5	conclusive
GCA_018657385.1	s__JABHXF01 sp018657385	79.8478	212	497	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__DSVV01;g__JABHXF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:47:11,196] [INFO] GTDB search result was written to OceanDNA-a1354/result_gtdb.tsv
[2023-03-15 17:47:11,197] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:47:11,197] [INFO] DFAST_QC result json was written to OceanDNA-a1354/dqc_result.json
[2023-03-15 17:47:11,197] [INFO] DFAST_QC completed!
[2023-03-15 17:47:11,197] [INFO] Total running time: 0h0m40s