[2023-03-19 01:50:01,577] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,577] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,577] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa9494c6-0685-42db-adbf-6186dc071f24/dqc_reference
[2023-03-19 01:50:02,660] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:02,661] [INFO] Task started: Prodigal
[2023-03-19 01:50:02,661] [INFO] Running command: cat /var/lib/cwl/stgf163327f-2758-499b-9b06-41f3610bb42c/OceanDNA-b24882.fa | prodigal -d OceanDNA-b24882/cds.fna -a OceanDNA-b24882/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:14,684] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:14,684] [INFO] Task started: HMMsearch
[2023-03-19 01:50:14,684] [INFO] Running command: hmmsearch --tblout OceanDNA-b24882/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa9494c6-0685-42db-adbf-6186dc071f24/dqc_reference/reference_markers.hmm OceanDNA-b24882/protein.faa > /dev/null
[2023-03-19 01:50:14,866] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:14,866] [INFO] Found 6/6 markers.
[2023-03-19 01:50:14,883] [INFO] Query marker FASTA was written to OceanDNA-b24882/markers.fasta
[2023-03-19 01:50:14,884] [INFO] Task started: Blastn
[2023-03-19 01:50:14,885] [INFO] Running command: blastn -query OceanDNA-b24882/markers.fasta -db /var/lib/cwl/stgfa9494c6-0685-42db-adbf-6186dc071f24/dqc_reference/reference_markers.fasta -out OceanDNA-b24882/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:15,440] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:15,441] [INFO] Selected 23 target genomes.
[2023-03-19 01:50:15,441] [INFO] Target genome list was writen to OceanDNA-b24882/target_genomes.txt
[2023-03-19 01:50:15,464] [INFO] Task started: fastANI
[2023-03-19 01:50:15,464] [INFO] Running command: fastANI --query /var/lib/cwl/stgf163327f-2758-499b-9b06-41f3610bb42c/OceanDNA-b24882.fa --refList OceanDNA-b24882/target_genomes.txt --output OceanDNA-b24882/fastani_result.tsv --threads 1
[2023-03-19 01:50:27,639] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:27,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa9494c6-0685-42db-adbf-6186dc071f24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:27,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa9494c6-0685-42db-adbf-6186dc071f24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:27,639] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:27,639] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:50:27,639] [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
--------------------------------------------------------------------------------
[2023-03-19 01:50:27,640] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24882/tc_result.tsv
[2023-03-19 01:50:27,640] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:27,640] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:27,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa9494c6-0685-42db-adbf-6186dc071f24/dqc_reference/checkm_data
[2023-03-19 01:50:27,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:27,647] [INFO] Task started: CheckM
[2023-03-19 01:50:27,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24882/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24882/checkm_input OceanDNA-b24882/checkm_result
[2023-03-19 01:51:01,930] [INFO] Task succeeded: CheckM
[2023-03-19 01:51:01,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:51:01,932] [INFO] ===== Completeness check finished =====
[2023-03-19 01:51:01,932] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:51:01,932] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24882/markers.fasta)
[2023-03-19 01:51:01,933] [INFO] Task started: Blastn
[2023-03-19 01:51:01,933] [INFO] Running command: blastn -query OceanDNA-b24882/markers.fasta -db /var/lib/cwl/stgfa9494c6-0685-42db-adbf-6186dc071f24/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24882/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:51:02,828] [INFO] Task succeeded: Blastn
[2023-03-19 01:51:02,828] [INFO] Selected 28 target genomes.
[2023-03-19 01:51:02,828] [INFO] Target genome list was writen to OceanDNA-b24882/target_genomes_gtdb.txt
[2023-03-19 01:51:02,846] [INFO] Task started: fastANI
[2023-03-19 01:51:02,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgf163327f-2758-499b-9b06-41f3610bb42c/OceanDNA-b24882.fa --refList OceanDNA-b24882/target_genomes_gtdb.txt --output OceanDNA-b24882/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:51:17,645] [INFO] Task succeeded: fastANI
[2023-03-19 01:51:17,647] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:51:17,647] [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_002401305.2	s__NORP139 sp002401305	82.201	235	604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__NORP139	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:51:17,647] [INFO] GTDB search result was written to OceanDNA-b24882/result_gtdb.tsv
[2023-03-19 01:51:17,647] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:51:17,647] [INFO] DFAST_QC result json was written to OceanDNA-b24882/dqc_result.json
[2023-03-19 01:51:17,647] [INFO] DFAST_QC completed!
[2023-03-19 01:51:17,647] [INFO] Total running time: 0h1m16s