[2023-03-15 22:06:34,880] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:06:34,880] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:06:34,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fd3f09f-6f2d-479b-8fab-29958fd3f3fb/dqc_reference
[2023-03-15 22:06:36,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:06:36,026] [INFO] Task started: Prodigal
[2023-03-15 22:06:36,026] [INFO] Running command: cat /var/lib/cwl/stg4c609be4-7c4c-4eb4-a233-2c7716e70d01/OceanDNA-b33212.fa | prodigal -d OceanDNA-b33212/cds.fna -a OceanDNA-b33212/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:06:51,223] [INFO] Task succeeded: Prodigal
[2023-03-15 22:06:51,223] [INFO] Task started: HMMsearch
[2023-03-15 22:06:51,223] [INFO] Running command: hmmsearch --tblout OceanDNA-b33212/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fd3f09f-6f2d-479b-8fab-29958fd3f3fb/dqc_reference/reference_markers.hmm OceanDNA-b33212/protein.faa > /dev/null
[2023-03-15 22:06:51,398] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:06:51,398] [INFO] Found 6/6 markers.
[2023-03-15 22:06:51,412] [INFO] Query marker FASTA was written to OceanDNA-b33212/markers.fasta
[2023-03-15 22:06:51,414] [INFO] Task started: Blastn
[2023-03-15 22:06:51,414] [INFO] Running command: blastn -query OceanDNA-b33212/markers.fasta -db /var/lib/cwl/stg0fd3f09f-6f2d-479b-8fab-29958fd3f3fb/dqc_reference/reference_markers.fasta -out OceanDNA-b33212/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:06:52,046] [INFO] Task succeeded: Blastn
[2023-03-15 22:06:52,046] [INFO] Selected 35 target genomes.
[2023-03-15 22:06:52,047] [INFO] Target genome list was writen to OceanDNA-b33212/target_genomes.txt
[2023-03-15 22:06:52,107] [INFO] Task started: fastANI
[2023-03-15 22:06:52,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c609be4-7c4c-4eb4-a233-2c7716e70d01/OceanDNA-b33212.fa --refList OceanDNA-b33212/target_genomes.txt --output OceanDNA-b33212/fastani_result.tsv --threads 1
[2023-03-15 22:07:16,084] [INFO] Task succeeded: fastANI
[2023-03-15 22:07:16,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fd3f09f-6f2d-479b-8fab-29958fd3f3fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:07:16,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fd3f09f-6f2d-479b-8fab-29958fd3f3fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:07:16,085] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:07:16,085] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:07:16,085] [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 22:07:16,088] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33212/tc_result.tsv
[2023-03-15 22:07:16,095] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:07:16,095] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:07:16,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fd3f09f-6f2d-479b-8fab-29958fd3f3fb/dqc_reference/checkm_data
[2023-03-15 22:07:16,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:07:16,103] [INFO] Task started: CheckM
[2023-03-15 22:07:16,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33212/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33212/checkm_input OceanDNA-b33212/checkm_result
[2023-03-15 22:07:56,586] [INFO] Task succeeded: CheckM
[2023-03-15 22:07:56,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:07:56,601] [INFO] ===== Completeness check finished =====
[2023-03-15 22:07:56,602] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:07:56,602] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33212/markers.fasta)
[2023-03-15 22:07:56,603] [INFO] Task started: Blastn
[2023-03-15 22:07:56,603] [INFO] Running command: blastn -query OceanDNA-b33212/markers.fasta -db /var/lib/cwl/stg0fd3f09f-6f2d-479b-8fab-29958fd3f3fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33212/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:07:57,706] [INFO] Task succeeded: Blastn
[2023-03-15 22:07:57,707] [INFO] Selected 34 target genomes.
[2023-03-15 22:07:57,707] [INFO] Target genome list was writen to OceanDNA-b33212/target_genomes_gtdb.txt
[2023-03-15 22:07:58,048] [INFO] Task started: fastANI
[2023-03-15 22:07:58,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c609be4-7c4c-4eb4-a233-2c7716e70d01/OceanDNA-b33212.fa --refList OceanDNA-b33212/target_genomes_gtdb.txt --output OceanDNA-b33212/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:08:19,366] [INFO] Task succeeded: fastANI
[2023-03-15 22:08:19,368] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:08:19,368] [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_002840095.1	s__Sulfurivermis sp002840095	75.7652	54	788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461825.1	s__Rugamonas sp016461825	75.4443	54	788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:08:19,369] [INFO] GTDB search result was written to OceanDNA-b33212/result_gtdb.tsv
[2023-03-15 22:08:19,369] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:08:19,369] [INFO] DFAST_QC result json was written to OceanDNA-b33212/dqc_result.json
[2023-03-15 22:08:19,369] [INFO] DFAST_QC completed!
[2023-03-15 22:08:19,369] [INFO] Total running time: 0h1m44s