[2023-03-15 08:11:06,015] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:11:06,015] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:11:06,015] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2c1c51a-06a9-4137-a8cb-2243ea2ac0ba/dqc_reference
[2023-03-15 08:11:07,130] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:11:07,130] [INFO] Task started: Prodigal
[2023-03-15 08:11:07,130] [INFO] Running command: cat /var/lib/cwl/stg0da71e13-de57-4ed2-8ed1-cc22b3b6c39f/OceanDNA-b32502.fa | prodigal -d OceanDNA-b32502/cds.fna -a OceanDNA-b32502/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:11:09,866] [INFO] Task succeeded: Prodigal
[2023-03-15 08:11:09,866] [INFO] Task started: HMMsearch
[2023-03-15 08:11:09,866] [INFO] Running command: hmmsearch --tblout OceanDNA-b32502/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2c1c51a-06a9-4137-a8cb-2243ea2ac0ba/dqc_reference/reference_markers.hmm OceanDNA-b32502/protein.faa > /dev/null
[2023-03-15 08:11:10,030] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:11:10,031] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0da71e13-de57-4ed2-8ed1-cc22b3b6c39f/OceanDNA-b32502.fa]
[2023-03-15 08:11:10,045] [INFO] Query marker FASTA was written to OceanDNA-b32502/markers.fasta
[2023-03-15 08:11:10,045] [INFO] Task started: Blastn
[2023-03-15 08:11:10,046] [INFO] Running command: blastn -query OceanDNA-b32502/markers.fasta -db /var/lib/cwl/stgb2c1c51a-06a9-4137-a8cb-2243ea2ac0ba/dqc_reference/reference_markers.fasta -out OceanDNA-b32502/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:10,597] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:10,598] [INFO] Selected 15 target genomes.
[2023-03-15 08:11:10,598] [INFO] Target genome list was writen to OceanDNA-b32502/target_genomes.txt
[2023-03-15 08:11:10,609] [INFO] Task started: fastANI
[2023-03-15 08:11:10,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg0da71e13-de57-4ed2-8ed1-cc22b3b6c39f/OceanDNA-b32502.fa --refList OceanDNA-b32502/target_genomes.txt --output OceanDNA-b32502/fastani_result.tsv --threads 1
[2023-03-15 08:11:16,221] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:16,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2c1c51a-06a9-4137-a8cb-2243ea2ac0ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:11:16,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2c1c51a-06a9-4137-a8cb-2243ea2ac0ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:11:16,222] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:11:16,222] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:11:16,222] [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 08:11:16,229] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32502/tc_result.tsv
[2023-03-15 08:11:16,233] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:11:16,234] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:11:16,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2c1c51a-06a9-4137-a8cb-2243ea2ac0ba/dqc_reference/checkm_data
[2023-03-15 08:11:16,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:11:16,259] [INFO] Task started: CheckM
[2023-03-15 08:11:16,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32502/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32502/checkm_input OceanDNA-b32502/checkm_result
[2023-03-15 08:11:30,493] [INFO] Task succeeded: CheckM
[2023-03-15 08:11:30,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.51%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:11:30,521] [INFO] ===== Completeness check finished =====
[2023-03-15 08:11:30,521] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:11:30,521] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32502/markers.fasta)
[2023-03-15 08:11:30,523] [INFO] Task started: Blastn
[2023-03-15 08:11:30,523] [INFO] Running command: blastn -query OceanDNA-b32502/markers.fasta -db /var/lib/cwl/stgb2c1c51a-06a9-4137-a8cb-2243ea2ac0ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32502/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:31,526] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:31,553] [INFO] Selected 30 target genomes.
[2023-03-15 08:11:31,553] [INFO] Target genome list was writen to OceanDNA-b32502/target_genomes_gtdb.txt
[2023-03-15 08:11:31,570] [INFO] Task started: fastANI
[2023-03-15 08:11:31,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg0da71e13-de57-4ed2-8ed1-cc22b3b6c39f/OceanDNA-b32502.fa --refList OceanDNA-b32502/target_genomes_gtdb.txt --output OceanDNA-b32502/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:11:37,630] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:37,632] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:11:37,632] [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_002167215.1	s__GCA-2691245 sp002167215	77.0961	52	165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	97.98	96.11	0.71	0.71	3	-
--------------------------------------------------------------------------------
[2023-03-15 08:11:37,632] [INFO] GTDB search result was written to OceanDNA-b32502/result_gtdb.tsv
[2023-03-15 08:11:37,632] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:11:37,633] [INFO] DFAST_QC result json was written to OceanDNA-b32502/dqc_result.json
[2023-03-15 08:11:37,633] [INFO] DFAST_QC completed!
[2023-03-15 08:11:37,633] [INFO] Total running time: 0h0m32s