[2023-03-18 08:31:56,320] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:31:56,320] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:31:56,320] [INFO] DQC Reference Directory: /var/lib/cwl/stg37cb3ea4-4de8-494f-9244-b29743ab46e2/dqc_reference
[2023-03-18 08:31:57,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:31:57,421] [INFO] Task started: Prodigal
[2023-03-18 08:31:57,421] [INFO] Running command: cat /var/lib/cwl/stgea59cf10-d7cc-4a8a-9b0a-88cbfa4cdb91/OceanDNA-b24206.fa | prodigal -d OceanDNA-b24206/cds.fna -a OceanDNA-b24206/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:31:59,279] [INFO] Task succeeded: Prodigal
[2023-03-18 08:31:59,280] [INFO] Task started: HMMsearch
[2023-03-18 08:31:59,280] [INFO] Running command: hmmsearch --tblout OceanDNA-b24206/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37cb3ea4-4de8-494f-9244-b29743ab46e2/dqc_reference/reference_markers.hmm OceanDNA-b24206/protein.faa > /dev/null
[2023-03-18 08:31:59,428] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:31:59,428] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgea59cf10-d7cc-4a8a-9b0a-88cbfa4cdb91/OceanDNA-b24206.fa]
[2023-03-18 08:31:59,433] [INFO] Query marker FASTA was written to OceanDNA-b24206/markers.fasta
[2023-03-18 08:31:59,435] [INFO] Task started: Blastn
[2023-03-18 08:31:59,435] [INFO] Running command: blastn -query OceanDNA-b24206/markers.fasta -db /var/lib/cwl/stg37cb3ea4-4de8-494f-9244-b29743ab46e2/dqc_reference/reference_markers.fasta -out OceanDNA-b24206/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:00,205] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:00,206] [INFO] Selected 13 target genomes.
[2023-03-18 08:32:00,206] [INFO] Target genome list was writen to OceanDNA-b24206/target_genomes.txt
[2023-03-18 08:32:00,213] [INFO] Task started: fastANI
[2023-03-18 08:32:00,213] [INFO] Running command: fastANI --query /var/lib/cwl/stgea59cf10-d7cc-4a8a-9b0a-88cbfa4cdb91/OceanDNA-b24206.fa --refList OceanDNA-b24206/target_genomes.txt --output OceanDNA-b24206/fastani_result.tsv --threads 1
[2023-03-18 08:32:05,241] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:05,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37cb3ea4-4de8-494f-9244-b29743ab46e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:32:05,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37cb3ea4-4de8-494f-9244-b29743ab46e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:32:05,241] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:32:05,241] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:32:05,242] [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
--------------------------------------------------------------------------------
[2023-03-18 08:32:05,242] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24206/tc_result.tsv
[2023-03-18 08:32:05,242] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:32:05,242] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:32:05,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37cb3ea4-4de8-494f-9244-b29743ab46e2/dqc_reference/checkm_data
[2023-03-18 08:32:05,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:32:05,246] [INFO] Task started: CheckM
[2023-03-18 08:32:05,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24206/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24206/checkm_input OceanDNA-b24206/checkm_result
[2023-03-18 08:32:19,320] [INFO] Task succeeded: CheckM
[2023-03-18 08:32:19,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:32:19,321] [INFO] ===== Completeness check finished =====
[2023-03-18 08:32:19,321] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:32:19,321] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24206/markers.fasta)
[2023-03-18 08:32:19,323] [INFO] Task started: Blastn
[2023-03-18 08:32:19,323] [INFO] Running command: blastn -query OceanDNA-b24206/markers.fasta -db /var/lib/cwl/stg37cb3ea4-4de8-494f-9244-b29743ab46e2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24206/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:20,412] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:20,412] [INFO] Selected 15 target genomes.
[2023-03-18 08:32:20,412] [INFO] Target genome list was writen to OceanDNA-b24206/target_genomes_gtdb.txt
[2023-03-18 08:32:20,432] [INFO] Task started: fastANI
[2023-03-18 08:32:20,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgea59cf10-d7cc-4a8a-9b0a-88cbfa4cdb91/OceanDNA-b24206.fa --refList OceanDNA-b24206/target_genomes_gtdb.txt --output OceanDNA-b24206/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:32:23,352] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:23,355] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:32:23,355] [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_902607475.1	s__GCA-002720895 sp902607475	83.1163	69	103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717245.1	s__GCA-002720895 sp002717245	79.4825	83	103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.29	99.29	0.96	0.96	2	-
GCA_002937775.1	s__GCA-002720895 sp002937775	78.9679	58	103	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.14	99.14	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:32:23,355] [INFO] GTDB search result was written to OceanDNA-b24206/result_gtdb.tsv
[2023-03-18 08:32:23,355] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:32:23,356] [INFO] DFAST_QC result json was written to OceanDNA-b24206/dqc_result.json
[2023-03-18 08:32:23,356] [INFO] DFAST_QC completed!
[2023-03-18 08:32:23,356] [INFO] Total running time: 0h0m27s