[2023-03-17 07:01:51,157] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:51,157] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:51,157] [INFO] DQC Reference Directory: /var/lib/cwl/stg37d037d0-1162-4c3e-b7c2-d33996f97344/dqc_reference
[2023-03-17 07:01:52,321] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:52,321] [INFO] Task started: Prodigal
[2023-03-17 07:01:52,321] [INFO] Running command: cat /var/lib/cwl/stg1cbbcb44-da1b-4567-bdcc-be9b0e9d5bf2/OceanDNA-b26067.fa | prodigal -d OceanDNA-b26067/cds.fna -a OceanDNA-b26067/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:01:59,469] [INFO] Task succeeded: Prodigal
[2023-03-17 07:01:59,470] [INFO] Task started: HMMsearch
[2023-03-17 07:01:59,470] [INFO] Running command: hmmsearch --tblout OceanDNA-b26067/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37d037d0-1162-4c3e-b7c2-d33996f97344/dqc_reference/reference_markers.hmm OceanDNA-b26067/protein.faa > /dev/null
[2023-03-17 07:01:59,638] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:01:59,639] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1cbbcb44-da1b-4567-bdcc-be9b0e9d5bf2/OceanDNA-b26067.fa]
[2023-03-17 07:01:59,651] [INFO] Query marker FASTA was written to OceanDNA-b26067/markers.fasta
[2023-03-17 07:01:59,651] [INFO] Task started: Blastn
[2023-03-17 07:01:59,651] [INFO] Running command: blastn -query OceanDNA-b26067/markers.fasta -db /var/lib/cwl/stg37d037d0-1162-4c3e-b7c2-d33996f97344/dqc_reference/reference_markers.fasta -out OceanDNA-b26067/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:00,158] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:00,207] [INFO] Selected 16 target genomes.
[2023-03-17 07:02:00,208] [INFO] Target genome list was writen to OceanDNA-b26067/target_genomes.txt
[2023-03-17 07:02:00,216] [INFO] Task started: fastANI
[2023-03-17 07:02:00,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cbbcb44-da1b-4567-bdcc-be9b0e9d5bf2/OceanDNA-b26067.fa --refList OceanDNA-b26067/target_genomes.txt --output OceanDNA-b26067/fastani_result.tsv --threads 1
[2023-03-17 07:02:05,507] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:05,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37d037d0-1162-4c3e-b7c2-d33996f97344/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:05,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37d037d0-1162-4c3e-b7c2-d33996f97344/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:05,508] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:05,508] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:02:05,508] [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
--------------------------------------------------------------------------------
[2023-03-17 07:02:05,509] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26067/tc_result.tsv
[2023-03-17 07:02:05,509] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:05,509] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:05,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37d037d0-1162-4c3e-b7c2-d33996f97344/dqc_reference/checkm_data
[2023-03-17 07:02:05,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:05,514] [INFO] Task started: CheckM
[2023-03-17 07:02:05,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26067/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26067/checkm_input OceanDNA-b26067/checkm_result
[2023-03-17 07:02:28,397] [INFO] Task succeeded: CheckM
[2023-03-17 07:02:28,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.91%
Contamintation: 2.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 07:02:28,399] [INFO] ===== Completeness check finished =====
[2023-03-17 07:02:28,399] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:02:28,399] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26067/markers.fasta)
[2023-03-17 07:02:28,399] [INFO] Task started: Blastn
[2023-03-17 07:02:28,399] [INFO] Running command: blastn -query OceanDNA-b26067/markers.fasta -db /var/lib/cwl/stg37d037d0-1162-4c3e-b7c2-d33996f97344/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26067/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:29,130] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:29,131] [INFO] Selected 26 target genomes.
[2023-03-17 07:02:29,131] [INFO] Target genome list was writen to OceanDNA-b26067/target_genomes_gtdb.txt
[2023-03-17 07:02:29,681] [INFO] Task started: fastANI
[2023-03-17 07:02:29,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cbbcb44-da1b-4567-bdcc-be9b0e9d5bf2/OceanDNA-b26067.fa --refList OceanDNA-b26067/target_genomes_gtdb.txt --output OceanDNA-b26067/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:02:36,665] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:36,669] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:02:36,669] [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_902532475.1	s__GCA-002684695 sp902532475	90.8295	286	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902522415.1	s__GCA-002684695 sp902522415	77.0926	53	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902539295.1	s__GCA-002684695 sp902539295	76.7529	92	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902612965.1	s__GCA-002684695 sp902612965	76.6768	97	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	96.38	96.38	0.79	0.79	2	-
GCA_002684695.1	s__GCA-002684695 sp002684695	76.5185	105	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__GCA-002684695;g__GCA-002684695	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:02:36,669] [INFO] GTDB search result was written to OceanDNA-b26067/result_gtdb.tsv
[2023-03-17 07:02:36,669] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:02:36,670] [INFO] DFAST_QC result json was written to OceanDNA-b26067/dqc_result.json
[2023-03-17 07:02:36,670] [INFO] DFAST_QC completed!
[2023-03-17 07:02:36,670] [INFO] Total running time: 0h0m46s