[2023-03-15 21:01:44,378] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,378] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,378] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a61cdf9-9db4-40e3-9436-2a3255cc49a5/dqc_reference
[2023-03-15 21:01:45,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,702] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,702] [INFO] Running command: cat /var/lib/cwl/stgca76e038-a130-452e-9f82-29be38de39af/OceanDNA-b38874.fa | prodigal -d OceanDNA-b38874/cds.fna -a OceanDNA-b38874/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:01:53,129] [INFO] Task succeeded: Prodigal
[2023-03-15 21:01:53,130] [INFO] Task started: HMMsearch
[2023-03-15 21:01:53,130] [INFO] Running command: hmmsearch --tblout OceanDNA-b38874/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a61cdf9-9db4-40e3-9436-2a3255cc49a5/dqc_reference/reference_markers.hmm OceanDNA-b38874/protein.faa > /dev/null
[2023-03-15 21:01:53,291] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:01:53,291] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgca76e038-a130-452e-9f82-29be38de39af/OceanDNA-b38874.fa]
[2023-03-15 21:01:53,310] [INFO] Query marker FASTA was written to OceanDNA-b38874/markers.fasta
[2023-03-15 21:01:53,310] [INFO] Task started: Blastn
[2023-03-15 21:01:53,310] [INFO] Running command: blastn -query OceanDNA-b38874/markers.fasta -db /var/lib/cwl/stg3a61cdf9-9db4-40e3-9436-2a3255cc49a5/dqc_reference/reference_markers.fasta -out OceanDNA-b38874/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:01:53,761] [INFO] Task succeeded: Blastn
[2023-03-15 21:01:53,762] [INFO] Selected 22 target genomes.
[2023-03-15 21:01:53,762] [INFO] Target genome list was writen to OceanDNA-b38874/target_genomes.txt
[2023-03-15 21:01:53,774] [INFO] Task started: fastANI
[2023-03-15 21:01:53,774] [INFO] Running command: fastANI --query /var/lib/cwl/stgca76e038-a130-452e-9f82-29be38de39af/OceanDNA-b38874.fa --refList OceanDNA-b38874/target_genomes.txt --output OceanDNA-b38874/fastani_result.tsv --threads 1
[2023-03-15 21:02:07,529] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:07,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a61cdf9-9db4-40e3-9436-2a3255cc49a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:07,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a61cdf9-9db4-40e3-9436-2a3255cc49a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:07,532] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 21:02:07,532] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 21:02:07,532] [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
Neptunomonas phycophila	strain=CECT 8716	GCA_001922575.1	1572645	1572645	type	True	98.4257	291	295	95	conclusive
--------------------------------------------------------------------------------
[2023-03-15 21:02:07,532] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38874/tc_result.tsv
[2023-03-15 21:02:07,532] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:07,532] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:07,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a61cdf9-9db4-40e3-9436-2a3255cc49a5/dqc_reference/checkm_data
[2023-03-15 21:02:07,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:07,537] [INFO] Task started: CheckM
[2023-03-15 21:02:07,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38874/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38874/checkm_input OceanDNA-b38874/checkm_result
[2023-03-15 21:02:31,912] [INFO] Task succeeded: CheckM
[2023-03-15 21:02:31,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.32%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:02:31,914] [INFO] ===== Completeness check finished =====
[2023-03-15 21:02:31,915] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:02:31,915] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38874/markers.fasta)
[2023-03-15 21:02:31,915] [INFO] Task started: Blastn
[2023-03-15 21:02:31,915] [INFO] Running command: blastn -query OceanDNA-b38874/markers.fasta -db /var/lib/cwl/stg3a61cdf9-9db4-40e3-9436-2a3255cc49a5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38874/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:32,401] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:32,402] [INFO] Selected 21 target genomes.
[2023-03-15 21:02:32,402] [INFO] Target genome list was writen to OceanDNA-b38874/target_genomes_gtdb.txt
[2023-03-15 21:02:32,804] [INFO] Task started: fastANI
[2023-03-15 21:02:32,804] [INFO] Running command: fastANI --query /var/lib/cwl/stgca76e038-a130-452e-9f82-29be38de39af/OceanDNA-b38874.fa --refList OceanDNA-b38874/target_genomes_gtdb.txt --output OceanDNA-b38874/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:02:44,413] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:44,415] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:02:44,415] [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
GCF_001922575.1	s__Neptunomonas phycophila	98.4257	291	295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	98.55	98.14	0.96	0.94	4	conclusive
--------------------------------------------------------------------------------
[2023-03-15 21:02:44,415] [INFO] GTDB search result was written to OceanDNA-b38874/result_gtdb.tsv
[2023-03-15 21:02:44,415] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:02:44,416] [INFO] DFAST_QC result json was written to OceanDNA-b38874/dqc_result.json
[2023-03-15 21:02:44,416] [INFO] DFAST_QC completed!
[2023-03-15 21:02:44,416] [INFO] Total running time: 0h1m0s