[2023-03-17 13:01:51,446] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,446] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,447] [INFO] DQC Reference Directory: /var/lib/cwl/stgba5f7822-8839-498c-b784-3be9011997b7/dqc_reference
[2023-03-17 13:01:52,736] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:52,736] [INFO] Task started: Prodigal
[2023-03-17 13:01:52,736] [INFO] Running command: cat /var/lib/cwl/stg8ad5af3f-287c-4415-9e89-4b4bd1656804/OceanDNA-b39227.fa | prodigal -d OceanDNA-b39227/cds.fna -a OceanDNA-b39227/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:01:59,366] [INFO] Task succeeded: Prodigal
[2023-03-17 13:01:59,366] [INFO] Task started: HMMsearch
[2023-03-17 13:01:59,366] [INFO] Running command: hmmsearch --tblout OceanDNA-b39227/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba5f7822-8839-498c-b784-3be9011997b7/dqc_reference/reference_markers.hmm OceanDNA-b39227/protein.faa > /dev/null
[2023-03-17 13:01:59,578] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:01:59,579] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8ad5af3f-287c-4415-9e89-4b4bd1656804/OceanDNA-b39227.fa]
[2023-03-17 13:01:59,591] [INFO] Query marker FASTA was written to OceanDNA-b39227/markers.fasta
[2023-03-17 13:01:59,591] [INFO] Task started: Blastn
[2023-03-17 13:01:59,591] [INFO] Running command: blastn -query OceanDNA-b39227/markers.fasta -db /var/lib/cwl/stgba5f7822-8839-498c-b784-3be9011997b7/dqc_reference/reference_markers.fasta -out OceanDNA-b39227/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:00,142] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:00,143] [INFO] Selected 26 target genomes.
[2023-03-17 13:02:00,143] [INFO] Target genome list was writen to OceanDNA-b39227/target_genomes.txt
[2023-03-17 13:02:00,162] [INFO] Task started: fastANI
[2023-03-17 13:02:00,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ad5af3f-287c-4415-9e89-4b4bd1656804/OceanDNA-b39227.fa --refList OceanDNA-b39227/target_genomes.txt --output OceanDNA-b39227/fastani_result.tsv --threads 1
[2023-03-17 13:02:13,999] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:14,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba5f7822-8839-498c-b784-3be9011997b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:14,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba5f7822-8839-498c-b784-3be9011997b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:14,000] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:14,000] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 13:02:14,000] [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 13:02:14,000] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39227/tc_result.tsv
[2023-03-17 13:02:14,000] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:14,000] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:14,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba5f7822-8839-498c-b784-3be9011997b7/dqc_reference/checkm_data
[2023-03-17 13:02:14,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:14,006] [INFO] Task started: CheckM
[2023-03-17 13:02:14,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39227/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39227/checkm_input OceanDNA-b39227/checkm_result
[2023-03-17 13:02:36,177] [INFO] Task succeeded: CheckM
[2023-03-17 13:02:36,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.33%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 13:02:36,179] [INFO] ===== Completeness check finished =====
[2023-03-17 13:02:36,180] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:02:36,180] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39227/markers.fasta)
[2023-03-17 13:02:36,180] [INFO] Task started: Blastn
[2023-03-17 13:02:36,180] [INFO] Running command: blastn -query OceanDNA-b39227/markers.fasta -db /var/lib/cwl/stgba5f7822-8839-498c-b784-3be9011997b7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39227/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:37,054] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:37,055] [INFO] Selected 25 target genomes.
[2023-03-17 13:02:37,055] [INFO] Target genome list was writen to OceanDNA-b39227/target_genomes_gtdb.txt
[2023-03-17 13:02:37,581] [INFO] Task started: fastANI
[2023-03-17 13:02:37,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ad5af3f-287c-4415-9e89-4b4bd1656804/OceanDNA-b39227.fa --refList OceanDNA-b39227/target_genomes_gtdb.txt --output OceanDNA-b39227/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:02:47,206] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:47,208] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 13:02:47,208] [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_002710745.1	s__AAA300-D14 sp002710745	98.7386	279	387	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__AAA300-D14	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902596775.1	s__AAA300-D14 sp002711285	91.8231	284	387	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__AAA300-D14	95.0	96.52	95.73	0.71	0.66	4	-
--------------------------------------------------------------------------------
[2023-03-17 13:02:47,208] [INFO] GTDB search result was written to OceanDNA-b39227/result_gtdb.tsv
[2023-03-17 13:02:47,209] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:02:47,209] [INFO] DFAST_QC result json was written to OceanDNA-b39227/dqc_result.json
[2023-03-17 13:02:47,209] [INFO] DFAST_QC completed!
[2023-03-17 13:02:47,209] [INFO] Total running time: 0h0m56s