[2023-03-15 17:46:31,581] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,581] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,581] [INFO] DQC Reference Directory: /var/lib/cwl/stg91d57484-8260-4024-9d11-5e5a40f2cece/dqc_reference
[2023-03-15 17:46:32,760] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,760] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,760] [INFO] Running command: cat /var/lib/cwl/stgf1a4a39c-0dc6-48bc-b2ba-2da95f6246ab/OceanDNA-b24650.fa | prodigal -d OceanDNA-b24650/cds.fna -a OceanDNA-b24650/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:44,910] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:44,911] [INFO] Task started: HMMsearch
[2023-03-15 17:46:44,911] [INFO] Running command: hmmsearch --tblout OceanDNA-b24650/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91d57484-8260-4024-9d11-5e5a40f2cece/dqc_reference/reference_markers.hmm OceanDNA-b24650/protein.faa > /dev/null
[2023-03-15 17:46:45,110] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:45,111] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf1a4a39c-0dc6-48bc-b2ba-2da95f6246ab/OceanDNA-b24650.fa]
[2023-03-15 17:46:45,130] [INFO] Query marker FASTA was written to OceanDNA-b24650/markers.fasta
[2023-03-15 17:46:45,131] [INFO] Task started: Blastn
[2023-03-15 17:46:45,132] [INFO] Running command: blastn -query OceanDNA-b24650/markers.fasta -db /var/lib/cwl/stg91d57484-8260-4024-9d11-5e5a40f2cece/dqc_reference/reference_markers.fasta -out OceanDNA-b24650/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:45,753] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:45,757] [INFO] Selected 30 target genomes.
[2023-03-15 17:46:45,757] [INFO] Target genome list was writen to OceanDNA-b24650/target_genomes.txt
[2023-03-15 17:46:45,775] [INFO] Task started: fastANI
[2023-03-15 17:46:45,775] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1a4a39c-0dc6-48bc-b2ba-2da95f6246ab/OceanDNA-b24650.fa --refList OceanDNA-b24650/target_genomes.txt --output OceanDNA-b24650/fastani_result.tsv --threads 1
[2023-03-15 17:47:04,701] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:04,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91d57484-8260-4024-9d11-5e5a40f2cece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:47:04,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91d57484-8260-4024-9d11-5e5a40f2cece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:47:04,702] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:47:04,702] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:47:04,702] [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 17:47:04,703] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24650/tc_result.tsv
[2023-03-15 17:47:04,703] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:47:04,704] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:47:04,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91d57484-8260-4024-9d11-5e5a40f2cece/dqc_reference/checkm_data
[2023-03-15 17:47:04,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:47:04,713] [INFO] Task started: CheckM
[2023-03-15 17:47:04,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24650/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24650/checkm_input OceanDNA-b24650/checkm_result
[2023-03-15 17:47:37,791] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:37,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:37,805] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:37,805] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:37,805] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24650/markers.fasta)
[2023-03-15 17:47:37,806] [INFO] Task started: Blastn
[2023-03-15 17:47:37,807] [INFO] Running command: blastn -query OceanDNA-b24650/markers.fasta -db /var/lib/cwl/stg91d57484-8260-4024-9d11-5e5a40f2cece/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24650/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:38,923] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:38,925] [INFO] Selected 27 target genomes.
[2023-03-15 17:47:38,925] [INFO] Target genome list was writen to OceanDNA-b24650/target_genomes_gtdb.txt
[2023-03-15 17:47:39,012] [INFO] Task started: fastANI
[2023-03-15 17:47:39,012] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1a4a39c-0dc6-48bc-b2ba-2da95f6246ab/OceanDNA-b24650.fa --refList OceanDNA-b24650/target_genomes_gtdb.txt --output OceanDNA-b24650/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:47:51,769] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:51,773] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:47:51,773] [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_002420015.1	s__UBA5701 sp002420015	76.5592	79	643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__UBA5701	95.0	99.49	99.43	0.89	0.88	3	-
GCA_002483465.1	s__UBA7657 sp002483465	76.3114	82	643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__UBA7657	95.0	99.02	98.94	0.94	0.93	3	-
GCA_016764775.1	s__TMED27 sp016764775	76.2783	59	643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__TMED27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696495.1	s__UBA7657 sp900696495	76.207	74	643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__UBA7657	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999645.1	s__UBA7657 sp017999645	76.0738	66	643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__UBA7657	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:47:51,775] [INFO] GTDB search result was written to OceanDNA-b24650/result_gtdb.tsv
[2023-03-15 17:47:51,776] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:47:51,778] [INFO] DFAST_QC result json was written to OceanDNA-b24650/dqc_result.json
[2023-03-15 17:47:51,778] [INFO] DFAST_QC completed!
[2023-03-15 17:47:51,778] [INFO] Total running time: 0h1m20s