[2023-03-15 23:15:05,777] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:15:05,778] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:15:05,778] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c87462d-4df9-4ef3-acbb-816f64227bd5/dqc_reference
[2023-03-15 23:15:07,540] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:15:07,541] [INFO] Task started: Prodigal
[2023-03-15 23:15:07,541] [INFO] Running command: cat /var/lib/cwl/stg7f2436a1-1220-4b84-a3f6-f81f5763b04c/OceanDNA-b15116.fa | prodigal -d OceanDNA-b15116/cds.fna -a OceanDNA-b15116/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:15:24,400] [INFO] Task succeeded: Prodigal
[2023-03-15 23:15:24,401] [INFO] Task started: HMMsearch
[2023-03-15 23:15:24,401] [INFO] Running command: hmmsearch --tblout OceanDNA-b15116/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c87462d-4df9-4ef3-acbb-816f64227bd5/dqc_reference/reference_markers.hmm OceanDNA-b15116/protein.faa > /dev/null
[2023-03-15 23:15:24,584] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:15:24,585] [INFO] Found 6/6 markers.
[2023-03-15 23:15:24,616] [INFO] Query marker FASTA was written to OceanDNA-b15116/markers.fasta
[2023-03-15 23:15:24,617] [INFO] Task started: Blastn
[2023-03-15 23:15:24,617] [INFO] Running command: blastn -query OceanDNA-b15116/markers.fasta -db /var/lib/cwl/stg8c87462d-4df9-4ef3-acbb-816f64227bd5/dqc_reference/reference_markers.fasta -out OceanDNA-b15116/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:15:25,141] [INFO] Task succeeded: Blastn
[2023-03-15 23:15:25,143] [INFO] Selected 11 target genomes.
[2023-03-15 23:15:25,144] [INFO] Target genome list was writen to OceanDNA-b15116/target_genomes.txt
[2023-03-15 23:15:25,151] [INFO] Task started: fastANI
[2023-03-15 23:15:25,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f2436a1-1220-4b84-a3f6-f81f5763b04c/OceanDNA-b15116.fa --refList OceanDNA-b15116/target_genomes.txt --output OceanDNA-b15116/fastani_result.tsv --threads 1
[2023-03-15 23:15:31,518] [INFO] Task succeeded: fastANI
[2023-03-15 23:15:31,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c87462d-4df9-4ef3-acbb-816f64227bd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:15:31,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c87462d-4df9-4ef3-acbb-816f64227bd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:15:31,519] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:15:31,519] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:15:31,519] [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 23:15:31,520] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15116/tc_result.tsv
[2023-03-15 23:15:31,521] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:15:31,521] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:15:31,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c87462d-4df9-4ef3-acbb-816f64227bd5/dqc_reference/checkm_data
[2023-03-15 23:15:31,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:15:31,529] [INFO] Task started: CheckM
[2023-03-15 23:15:31,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15116/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15116/checkm_input OceanDNA-b15116/checkm_result
[2023-03-15 23:16:16,039] [INFO] Task succeeded: CheckM
[2023-03-15 23:16:16,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:16:16,062] [INFO] ===== Completeness check finished =====
[2023-03-15 23:16:16,062] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:16:16,062] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15116/markers.fasta)
[2023-03-15 23:16:16,063] [INFO] Task started: Blastn
[2023-03-15 23:16:16,063] [INFO] Running command: blastn -query OceanDNA-b15116/markers.fasta -db /var/lib/cwl/stg8c87462d-4df9-4ef3-acbb-816f64227bd5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15116/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:16:16,813] [INFO] Task succeeded: Blastn
[2023-03-15 23:16:16,817] [INFO] Selected 14 target genomes.
[2023-03-15 23:16:16,817] [INFO] Target genome list was writen to OceanDNA-b15116/target_genomes_gtdb.txt
[2023-03-15 23:16:16,851] [INFO] Task started: fastANI
[2023-03-15 23:16:16,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f2436a1-1220-4b84-a3f6-f81f5763b04c/OceanDNA-b15116.fa --refList OceanDNA-b15116/target_genomes_gtdb.txt --output OceanDNA-b15116/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:16:24,226] [INFO] Task succeeded: fastANI
[2023-03-15 23:16:24,229] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:16:24,229] [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_002311865.1	s__UBA1151 sp002311865	79.9439	519	906	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__UBA1151	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204555.1	s__UBA1151 sp013204555	78.5179	441	906	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__UBA1151	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:16:24,230] [INFO] GTDB search result was written to OceanDNA-b15116/result_gtdb.tsv
[2023-03-15 23:16:24,231] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:16:24,234] [INFO] DFAST_QC result json was written to OceanDNA-b15116/dqc_result.json
[2023-03-15 23:16:24,234] [INFO] DFAST_QC completed!
[2023-03-15 23:16:24,234] [INFO] Total running time: 0h1m18s