[2023-03-15 08:09:45,340] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,340] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,340] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a4428c4-85e3-4161-beb8-e056c611b5c2/dqc_reference
[2023-03-15 08:09:46,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,589] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,589] [INFO] Running command: cat /var/lib/cwl/stgf2765c63-1a8b-49ad-a559-f7d38153e737/OceanDNA-b21685.fa | prodigal -d OceanDNA-b21685/cds.fna -a OceanDNA-b21685/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:09:50,700] [INFO] Task succeeded: Prodigal
[2023-03-15 08:09:50,700] [INFO] Task started: HMMsearch
[2023-03-15 08:09:50,700] [INFO] Running command: hmmsearch --tblout OceanDNA-b21685/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a4428c4-85e3-4161-beb8-e056c611b5c2/dqc_reference/reference_markers.hmm OceanDNA-b21685/protein.faa > /dev/null
[2023-03-15 08:09:50,935] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:09:50,935] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf2765c63-1a8b-49ad-a559-f7d38153e737/OceanDNA-b21685.fa]
[2023-03-15 08:09:50,942] [INFO] Query marker FASTA was written to OceanDNA-b21685/markers.fasta
[2023-03-15 08:09:50,943] [INFO] Task started: Blastn
[2023-03-15 08:09:50,943] [INFO] Running command: blastn -query OceanDNA-b21685/markers.fasta -db /var/lib/cwl/stg7a4428c4-85e3-4161-beb8-e056c611b5c2/dqc_reference/reference_markers.fasta -out OceanDNA-b21685/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:09:51,644] [INFO] Task succeeded: Blastn
[2023-03-15 08:09:51,645] [INFO] Selected 6 target genomes.
[2023-03-15 08:09:51,645] [INFO] Target genome list was writen to OceanDNA-b21685/target_genomes.txt
[2023-03-15 08:09:51,649] [INFO] Task started: fastANI
[2023-03-15 08:09:51,650] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2765c63-1a8b-49ad-a559-f7d38153e737/OceanDNA-b21685.fa --refList OceanDNA-b21685/target_genomes.txt --output OceanDNA-b21685/fastani_result.tsv --threads 1
[2023-03-15 08:09:55,088] [INFO] Task succeeded: fastANI
[2023-03-15 08:09:55,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a4428c4-85e3-4161-beb8-e056c611b5c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:09:55,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a4428c4-85e3-4161-beb8-e056c611b5c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:09:55,089] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:09:55,089] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:09:55,089] [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 08:09:55,090] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21685/tc_result.tsv
[2023-03-15 08:09:55,090] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:09:55,090] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:09:55,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a4428c4-85e3-4161-beb8-e056c611b5c2/dqc_reference/checkm_data
[2023-03-15 08:09:55,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:09:55,102] [INFO] Task started: CheckM
[2023-03-15 08:09:55,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21685/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21685/checkm_input OceanDNA-b21685/checkm_result
[2023-03-15 08:10:12,041] [INFO] Task succeeded: CheckM
[2023-03-15 08:10:12,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.26%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:10:12,043] [INFO] ===== Completeness check finished =====
[2023-03-15 08:10:12,043] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:10:12,043] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21685/markers.fasta)
[2023-03-15 08:10:12,044] [INFO] Task started: Blastn
[2023-03-15 08:10:12,044] [INFO] Running command: blastn -query OceanDNA-b21685/markers.fasta -db /var/lib/cwl/stg7a4428c4-85e3-4161-beb8-e056c611b5c2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21685/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:12,864] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:12,865] [INFO] Selected 17 target genomes.
[2023-03-15 08:10:12,865] [INFO] Target genome list was writen to OceanDNA-b21685/target_genomes_gtdb.txt
[2023-03-15 08:10:12,880] [INFO] Task started: fastANI
[2023-03-15 08:10:12,881] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2765c63-1a8b-49ad-a559-f7d38153e737/OceanDNA-b21685.fa --refList OceanDNA-b21685/target_genomes_gtdb.txt --output OceanDNA-b21685/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:10:16,760] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:16,763] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:10:16,763] [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_018657765.1	s__CG2-30-36-39 sp018657765	99.937	260	263	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__PJMF01;g__CG2-30-36-39	95.0	99.97	99.97	0.96	0.96	2	conclusive
GCA_001873435.1	s__CG2-30-36-39 sp001873435	77.1071	62	263	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__PJMF01;g__CG2-30-36-39	95.0	99.95	99.90	0.98	0.97	4	-
--------------------------------------------------------------------------------
[2023-03-15 08:10:16,763] [INFO] GTDB search result was written to OceanDNA-b21685/result_gtdb.tsv
[2023-03-15 08:10:16,764] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:10:16,764] [INFO] DFAST_QC result json was written to OceanDNA-b21685/dqc_result.json
[2023-03-15 08:10:16,764] [INFO] DFAST_QC completed!
[2023-03-15 08:10:16,764] [INFO] Total running time: 0h0m31s