[2023-03-16 20:37:55,689] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:37:55,689] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:37:55,690] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4a2c8fb-7f7d-43fb-9645-7b0839a8ca82/dqc_reference
[2023-03-16 20:37:57,566] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:37:57,566] [INFO] Task started: Prodigal
[2023-03-16 20:37:57,566] [INFO] Running command: cat /var/lib/cwl/stg3e1b6e56-9e1e-4427-9d17-7049408acca1/OceanDNA-b26057.fa | prodigal -d OceanDNA-b26057/cds.fna -a OceanDNA-b26057/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:38:04,588] [INFO] Task succeeded: Prodigal
[2023-03-16 20:38:04,588] [INFO] Task started: HMMsearch
[2023-03-16 20:38:04,588] [INFO] Running command: hmmsearch --tblout OceanDNA-b26057/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4a2c8fb-7f7d-43fb-9645-7b0839a8ca82/dqc_reference/reference_markers.hmm OceanDNA-b26057/protein.faa > /dev/null
[2023-03-16 20:38:04,968] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:38:04,969] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3e1b6e56-9e1e-4427-9d17-7049408acca1/OceanDNA-b26057.fa]
[2023-03-16 20:38:04,986] [INFO] Query marker FASTA was written to OceanDNA-b26057/markers.fasta
[2023-03-16 20:38:04,988] [INFO] Task started: Blastn
[2023-03-16 20:38:04,989] [INFO] Running command: blastn -query OceanDNA-b26057/markers.fasta -db /var/lib/cwl/stgd4a2c8fb-7f7d-43fb-9645-7b0839a8ca82/dqc_reference/reference_markers.fasta -out OceanDNA-b26057/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:38:06,098] [INFO] Task succeeded: Blastn
[2023-03-16 20:38:06,099] [INFO] Selected 11 target genomes.
[2023-03-16 20:38:06,100] [INFO] Target genome list was writen to OceanDNA-b26057/target_genomes.txt
[2023-03-16 20:38:06,107] [INFO] Task started: fastANI
[2023-03-16 20:38:06,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e1b6e56-9e1e-4427-9d17-7049408acca1/OceanDNA-b26057.fa --refList OceanDNA-b26057/target_genomes.txt --output OceanDNA-b26057/fastani_result.tsv --threads 1
[2023-03-16 20:38:14,388] [INFO] Task succeeded: fastANI
[2023-03-16 20:38:14,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4a2c8fb-7f7d-43fb-9645-7b0839a8ca82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:38:14,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4a2c8fb-7f7d-43fb-9645-7b0839a8ca82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:38:14,389] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:38:14,389] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 20:38:14,389] [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 20:38:14,389] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26057/tc_result.tsv
[2023-03-16 20:38:14,389] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:38:14,389] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:38:14,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4a2c8fb-7f7d-43fb-9645-7b0839a8ca82/dqc_reference/checkm_data
[2023-03-16 20:38:14,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:38:14,413] [INFO] Task started: CheckM
[2023-03-16 20:38:14,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26057/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26057/checkm_input OceanDNA-b26057/checkm_result
[2023-03-16 20:38:36,946] [INFO] Task succeeded: CheckM
[2023-03-16 20:38:36,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:38:36,950] [INFO] ===== Completeness check finished =====
[2023-03-16 20:38:36,950] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:38:36,950] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26057/markers.fasta)
[2023-03-16 20:38:36,952] [INFO] Task started: Blastn
[2023-03-16 20:38:36,952] [INFO] Running command: blastn -query OceanDNA-b26057/markers.fasta -db /var/lib/cwl/stgd4a2c8fb-7f7d-43fb-9645-7b0839a8ca82/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26057/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:38:37,776] [INFO] Task succeeded: Blastn
[2023-03-16 20:38:37,777] [INFO] Selected 14 target genomes.
[2023-03-16 20:38:37,778] [INFO] Target genome list was writen to OceanDNA-b26057/target_genomes_gtdb.txt
[2023-03-16 20:38:37,815] [INFO] Task started: fastANI
[2023-03-16 20:38:37,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e1b6e56-9e1e-4427-9d17-7049408acca1/OceanDNA-b26057.fa --refList OceanDNA-b26057/target_genomes_gtdb.txt --output OceanDNA-b26057/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:38:41,398] [INFO] Task succeeded: fastANI
[2023-03-16 20:38:41,401] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 20:38:41,401] [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_003213175.1	s__AG-426-I14 sp003213175	98.4445	211	360	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AG-426-I14	95.0	99.07	98.14	0.88	0.76	3	conclusive
GCA_003210055.1	s__AG-426-I14 sp003210055	92.7035	284	360	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AG-426-I14	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902533695.1	s__AG-426-I14 sp902533695	76.9578	78	360	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AG-426-I14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 20:38:41,402] [INFO] GTDB search result was written to OceanDNA-b26057/result_gtdb.tsv
[2023-03-16 20:38:41,402] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:38:41,403] [INFO] DFAST_QC result json was written to OceanDNA-b26057/dqc_result.json
[2023-03-16 20:38:41,403] [INFO] DFAST_QC completed!
[2023-03-16 20:38:41,403] [INFO] Total running time: 0h0m46s