[2023-03-17 00:02:20,747] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:02:20,747] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:02:20,747] [INFO] DQC Reference Directory: /var/lib/cwl/stga031a877-3a5b-48d0-bddb-06aa90632dba/dqc_reference
[2023-03-17 00:02:21,851] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:02:21,852] [INFO] Task started: Prodigal
[2023-03-17 00:02:21,852] [INFO] Running command: cat /var/lib/cwl/stg2fb3c91d-692d-448d-ae7f-0bd64ffbf5ba/OceanDNA-b28382.fa | prodigal -d OceanDNA-b28382/cds.fna -a OceanDNA-b28382/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:02:31,296] [INFO] Task succeeded: Prodigal
[2023-03-17 00:02:31,296] [INFO] Task started: HMMsearch
[2023-03-17 00:02:31,296] [INFO] Running command: hmmsearch --tblout OceanDNA-b28382/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga031a877-3a5b-48d0-bddb-06aa90632dba/dqc_reference/reference_markers.hmm OceanDNA-b28382/protein.faa > /dev/null
[2023-03-17 00:02:31,476] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:02:31,477] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2fb3c91d-692d-448d-ae7f-0bd64ffbf5ba/OceanDNA-b28382.fa]
[2023-03-17 00:02:31,491] [INFO] Query marker FASTA was written to OceanDNA-b28382/markers.fasta
[2023-03-17 00:02:31,492] [INFO] Task started: Blastn
[2023-03-17 00:02:31,492] [INFO] Running command: blastn -query OceanDNA-b28382/markers.fasta -db /var/lib/cwl/stga031a877-3a5b-48d0-bddb-06aa90632dba/dqc_reference/reference_markers.fasta -out OceanDNA-b28382/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:02:32,031] [INFO] Task succeeded: Blastn
[2023-03-17 00:02:32,032] [INFO] Selected 19 target genomes.
[2023-03-17 00:02:32,032] [INFO] Target genome list was writen to OceanDNA-b28382/target_genomes.txt
[2023-03-17 00:02:32,166] [INFO] Task started: fastANI
[2023-03-17 00:02:32,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb3c91d-692d-448d-ae7f-0bd64ffbf5ba/OceanDNA-b28382.fa --refList OceanDNA-b28382/target_genomes.txt --output OceanDNA-b28382/fastani_result.tsv --threads 1
[2023-03-17 00:02:40,212] [INFO] Task succeeded: fastANI
[2023-03-17 00:02:40,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga031a877-3a5b-48d0-bddb-06aa90632dba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:02:40,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga031a877-3a5b-48d0-bddb-06aa90632dba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:02:40,212] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:02:40,212] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:02:40,212] [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
--------------------------------------------------------------------------------
[2023-03-17 00:02:40,213] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28382/tc_result.tsv
[2023-03-17 00:02:40,213] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:02:40,213] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:02:40,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga031a877-3a5b-48d0-bddb-06aa90632dba/dqc_reference/checkm_data
[2023-03-17 00:02:40,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:02:40,380] [INFO] Task started: CheckM
[2023-03-17 00:02:40,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28382/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28382/checkm_input OceanDNA-b28382/checkm_result
[2023-03-17 00:03:08,591] [INFO] Task succeeded: CheckM
[2023-03-17 00:03:08,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 00:03:08,620] [INFO] ===== Completeness check finished =====
[2023-03-17 00:03:08,620] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:03:08,620] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28382/markers.fasta)
[2023-03-17 00:03:08,621] [INFO] Task started: Blastn
[2023-03-17 00:03:08,621] [INFO] Running command: blastn -query OceanDNA-b28382/markers.fasta -db /var/lib/cwl/stga031a877-3a5b-48d0-bddb-06aa90632dba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28382/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:03:09,434] [INFO] Task succeeded: Blastn
[2023-03-17 00:03:09,453] [INFO] Selected 22 target genomes.
[2023-03-17 00:03:09,453] [INFO] Target genome list was writen to OceanDNA-b28382/target_genomes_gtdb.txt
[2023-03-17 00:03:09,671] [INFO] Task started: fastANI
[2023-03-17 00:03:09,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb3c91d-692d-448d-ae7f-0bd64ffbf5ba/OceanDNA-b28382.fa --refList OceanDNA-b28382/target_genomes_gtdb.txt --output OceanDNA-b28382/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:03:16,216] [INFO] Task succeeded: fastANI
[2023-03-17 00:03:16,219] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:03:16,219] [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_002683355.1	s__GCA-002712045 sp002683355	98.6412	470	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-002712045	95.0	97.70	97.13	0.78	0.71	3	conclusive
GCA_002712045.1	s__GCA-002712045 sp002712045	79.7675	145	582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-002712045	95.0	96.83	95.42	0.85	0.80	3	-
--------------------------------------------------------------------------------
[2023-03-17 00:03:16,225] [INFO] GTDB search result was written to OceanDNA-b28382/result_gtdb.tsv
[2023-03-17 00:03:16,226] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:03:16,226] [INFO] DFAST_QC result json was written to OceanDNA-b28382/dqc_result.json
[2023-03-17 00:03:16,226] [INFO] DFAST_QC completed!
[2023-03-17 00:03:16,226] [INFO] Total running time: 0h0m55s