[2023-03-15 09:48:16,400] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,400] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c79ca20-df4e-458b-8ca6-ed764f6acf45/dqc_reference
[2023-03-15 09:48:18,052] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,054] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,054] [INFO] Running command: cat /var/lib/cwl/stg6806433f-9fc7-46b1-b65e-e7a8640fe970/OceanDNA-b32939.fa | prodigal -d OceanDNA-b32939/cds.fna -a OceanDNA-b32939/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:25,663] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:25,663] [INFO] Task started: HMMsearch
[2023-03-15 09:48:25,663] [INFO] Running command: hmmsearch --tblout OceanDNA-b32939/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c79ca20-df4e-458b-8ca6-ed764f6acf45/dqc_reference/reference_markers.hmm OceanDNA-b32939/protein.faa > /dev/null
[2023-03-15 09:48:25,839] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:25,839] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6806433f-9fc7-46b1-b65e-e7a8640fe970/OceanDNA-b32939.fa]
[2023-03-15 09:48:25,854] [INFO] Query marker FASTA was written to OceanDNA-b32939/markers.fasta
[2023-03-15 09:48:25,855] [INFO] Task started: Blastn
[2023-03-15 09:48:25,855] [INFO] Running command: blastn -query OceanDNA-b32939/markers.fasta -db /var/lib/cwl/stg3c79ca20-df4e-458b-8ca6-ed764f6acf45/dqc_reference/reference_markers.fasta -out OceanDNA-b32939/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:26,395] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:26,395] [INFO] Selected 19 target genomes.
[2023-03-15 09:48:26,396] [INFO] Target genome list was writen to OceanDNA-b32939/target_genomes.txt
[2023-03-15 09:48:26,416] [INFO] Task started: fastANI
[2023-03-15 09:48:26,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg6806433f-9fc7-46b1-b65e-e7a8640fe970/OceanDNA-b32939.fa --refList OceanDNA-b32939/target_genomes.txt --output OceanDNA-b32939/fastani_result.tsv --threads 1
[2023-03-15 09:48:38,543] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:38,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c79ca20-df4e-458b-8ca6-ed764f6acf45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:38,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c79ca20-df4e-458b-8ca6-ed764f6acf45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:38,544] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:38,544] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:38,544] [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 09:48:38,544] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32939/tc_result.tsv
[2023-03-15 09:48:38,545] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:38,545] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:38,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c79ca20-df4e-458b-8ca6-ed764f6acf45/dqc_reference/checkm_data
[2023-03-15 09:48:38,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:38,551] [INFO] Task started: CheckM
[2023-03-15 09:48:38,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32939/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32939/checkm_input OceanDNA-b32939/checkm_result
[2023-03-15 09:49:02,857] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:02,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:02,859] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:02,859] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:02,859] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32939/markers.fasta)
[2023-03-15 09:49:02,860] [INFO] Task started: Blastn
[2023-03-15 09:49:02,860] [INFO] Running command: blastn -query OceanDNA-b32939/markers.fasta -db /var/lib/cwl/stg3c79ca20-df4e-458b-8ca6-ed764f6acf45/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32939/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:03,562] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:03,563] [INFO] Selected 18 target genomes.
[2023-03-15 09:49:03,563] [INFO] Target genome list was writen to OceanDNA-b32939/target_genomes_gtdb.txt
[2023-03-15 09:49:03,914] [INFO] Task started: fastANI
[2023-03-15 09:49:03,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg6806433f-9fc7-46b1-b65e-e7a8640fe970/OceanDNA-b32939.fa --refList OceanDNA-b32939/target_genomes_gtdb.txt --output OceanDNA-b32939/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:14,208] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:14,211] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:49:14,211] [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_002937555.1	s__PTKB01 sp002937555	80.3127	166	318	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666805.1	s__PTKB01 sp018666805	77.842	183	318	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	99.32	99.22	0.89	0.88	8	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:14,211] [INFO] GTDB search result was written to OceanDNA-b32939/result_gtdb.tsv
[2023-03-15 09:49:14,211] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:14,212] [INFO] DFAST_QC result json was written to OceanDNA-b32939/dqc_result.json
[2023-03-15 09:49:14,212] [INFO] DFAST_QC completed!
[2023-03-15 09:49:14,212] [INFO] Total running time: 0h0m58s