[2023-03-15 21:01:46,293] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:46,293] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:46,293] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ea619a4-5f68-4661-89f1-c16af059b173/dqc_reference
[2023-03-15 21:01:47,388] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:47,388] [INFO] Task started: Prodigal
[2023-03-15 21:01:47,388] [INFO] Running command: cat /var/lib/cwl/stg43b4c2cf-62a9-4cfb-834e-a93222e61a37/OceanDNA-b33246.fa | prodigal -d OceanDNA-b33246/cds.fna -a OceanDNA-b33246/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:01:55,521] [INFO] Task succeeded: Prodigal
[2023-03-15 21:01:55,522] [INFO] Task started: HMMsearch
[2023-03-15 21:01:55,522] [INFO] Running command: hmmsearch --tblout OceanDNA-b33246/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ea619a4-5f68-4661-89f1-c16af059b173/dqc_reference/reference_markers.hmm OceanDNA-b33246/protein.faa > /dev/null
[2023-03-15 21:01:55,695] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:01:55,696] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg43b4c2cf-62a9-4cfb-834e-a93222e61a37/OceanDNA-b33246.fa]
[2023-03-15 21:01:55,707] [INFO] Query marker FASTA was written to OceanDNA-b33246/markers.fasta
[2023-03-15 21:01:55,707] [INFO] Task started: Blastn
[2023-03-15 21:01:55,707] [INFO] Running command: blastn -query OceanDNA-b33246/markers.fasta -db /var/lib/cwl/stg4ea619a4-5f68-4661-89f1-c16af059b173/dqc_reference/reference_markers.fasta -out OceanDNA-b33246/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:01:56,262] [INFO] Task succeeded: Blastn
[2023-03-15 21:01:56,263] [INFO] Selected 21 target genomes.
[2023-03-15 21:01:56,263] [INFO] Target genome list was writen to OceanDNA-b33246/target_genomes.txt
[2023-03-15 21:01:56,275] [INFO] Task started: fastANI
[2023-03-15 21:01:56,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg43b4c2cf-62a9-4cfb-834e-a93222e61a37/OceanDNA-b33246.fa --refList OceanDNA-b33246/target_genomes.txt --output OceanDNA-b33246/fastani_result.tsv --threads 1
[2023-03-15 21:02:08,311] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:08,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ea619a4-5f68-4661-89f1-c16af059b173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:08,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ea619a4-5f68-4661-89f1-c16af059b173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:08,312] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:08,312] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:02:08,312] [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 21:02:08,312] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33246/tc_result.tsv
[2023-03-15 21:02:08,312] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:08,312] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:08,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ea619a4-5f68-4661-89f1-c16af059b173/dqc_reference/checkm_data
[2023-03-15 21:02:08,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:08,318] [INFO] Task started: CheckM
[2023-03-15 21:02:08,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33246/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33246/checkm_input OceanDNA-b33246/checkm_result
[2023-03-15 21:02:33,398] [INFO] Task succeeded: CheckM
[2023-03-15 21:02:33,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:02:33,400] [INFO] ===== Completeness check finished =====
[2023-03-15 21:02:33,400] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:02:33,401] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33246/markers.fasta)
[2023-03-15 21:02:33,401] [INFO] Task started: Blastn
[2023-03-15 21:02:33,401] [INFO] Running command: blastn -query OceanDNA-b33246/markers.fasta -db /var/lib/cwl/stg4ea619a4-5f68-4661-89f1-c16af059b173/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33246/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:34,217] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:34,218] [INFO] Selected 25 target genomes.
[2023-03-15 21:02:34,218] [INFO] Target genome list was writen to OceanDNA-b33246/target_genomes_gtdb.txt
[2023-03-15 21:02:34,755] [INFO] Task started: fastANI
[2023-03-15 21:02:34,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg43b4c2cf-62a9-4cfb-834e-a93222e61a37/OceanDNA-b33246.fa --refList OceanDNA-b33246/target_genomes_gtdb.txt --output OceanDNA-b33246/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:02:47,995] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:47,997] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:02:47,997] [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_002708265.1	s__GCA-2708265 sp002708265	99.9921	471	494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Berkiellales;f__Berkiellaceae;g__GCA-2708265	95.0	99.94	99.94	0.90	0.90	2	conclusive
--------------------------------------------------------------------------------
[2023-03-15 21:02:47,997] [INFO] GTDB search result was written to OceanDNA-b33246/result_gtdb.tsv
[2023-03-15 21:02:47,997] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:02:47,997] [INFO] DFAST_QC result json was written to OceanDNA-b33246/dqc_result.json
[2023-03-15 21:02:47,998] [INFO] DFAST_QC completed!
[2023-03-15 21:02:47,998] [INFO] Total running time: 0h1m2s