[2023-03-14 12:13:42,663] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:13:42,663] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:13:42,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg984fdd70-a9b1-4b52-86d2-94d1a09cfe7b/dqc_reference
[2023-03-14 12:13:44,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:13:44,621] [INFO] Task started: Prodigal
[2023-03-14 12:13:44,621] [INFO] Running command: cat /var/lib/cwl/stg8c175013-1898-4270-b9af-099ac4c85138/OceanDNA-b15082.fa | prodigal -d OceanDNA-b15082/cds.fna -a OceanDNA-b15082/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:13:54,242] [INFO] Task succeeded: Prodigal
[2023-03-14 12:13:54,242] [INFO] Task started: HMMsearch
[2023-03-14 12:13:54,242] [INFO] Running command: hmmsearch --tblout OceanDNA-b15082/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg984fdd70-a9b1-4b52-86d2-94d1a09cfe7b/dqc_reference/reference_markers.hmm OceanDNA-b15082/protein.faa > /dev/null
[2023-03-14 12:13:54,400] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:13:54,401] [INFO] Found 6/6 markers.
[2023-03-14 12:13:54,414] [INFO] Query marker FASTA was written to OceanDNA-b15082/markers.fasta
[2023-03-14 12:13:54,415] [INFO] Task started: Blastn
[2023-03-14 12:13:54,415] [INFO] Running command: blastn -query OceanDNA-b15082/markers.fasta -db /var/lib/cwl/stg984fdd70-a9b1-4b52-86d2-94d1a09cfe7b/dqc_reference/reference_markers.fasta -out OceanDNA-b15082/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:13:54,945] [INFO] Task succeeded: Blastn
[2023-03-14 12:13:54,946] [INFO] Selected 19 target genomes.
[2023-03-14 12:13:54,946] [INFO] Target genome list was writen to OceanDNA-b15082/target_genomes.txt
[2023-03-14 12:13:54,958] [INFO] Task started: fastANI
[2023-03-14 12:13:54,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c175013-1898-4270-b9af-099ac4c85138/OceanDNA-b15082.fa --refList OceanDNA-b15082/target_genomes.txt --output OceanDNA-b15082/fastani_result.tsv --threads 1
[2023-03-14 12:14:08,630] [INFO] Task succeeded: fastANI
[2023-03-14 12:14:08,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg984fdd70-a9b1-4b52-86d2-94d1a09cfe7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:14:08,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg984fdd70-a9b1-4b52-86d2-94d1a09cfe7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:14:08,631] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:14:08,631] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:14:08,631] [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
--------------------------------------------------------------------------------
[2023-03-14 12:14:08,631] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15082/tc_result.tsv
[2023-03-14 12:14:08,632] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:14:08,632] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:14:08,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg984fdd70-a9b1-4b52-86d2-94d1a09cfe7b/dqc_reference/checkm_data
[2023-03-14 12:14:08,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:14:08,638] [INFO] Task started: CheckM
[2023-03-14 12:14:08,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15082/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15082/checkm_input OceanDNA-b15082/checkm_result
[2023-03-14 12:14:37,146] [INFO] Task succeeded: CheckM
[2023-03-14 12:14:37,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 6.51%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-03-14 12:14:37,161] [INFO] ===== Completeness check finished =====
[2023-03-14 12:14:37,161] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:14:37,161] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15082/markers.fasta)
[2023-03-14 12:14:37,162] [INFO] Task started: Blastn
[2023-03-14 12:14:37,162] [INFO] Running command: blastn -query OceanDNA-b15082/markers.fasta -db /var/lib/cwl/stg984fdd70-a9b1-4b52-86d2-94d1a09cfe7b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15082/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:14:37,933] [INFO] Task succeeded: Blastn
[2023-03-14 12:14:37,934] [INFO] Selected 17 target genomes.
[2023-03-14 12:14:37,935] [INFO] Target genome list was writen to OceanDNA-b15082/target_genomes_gtdb.txt
[2023-03-14 12:14:37,977] [INFO] Task started: fastANI
[2023-03-14 12:14:37,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c175013-1898-4270-b9af-099ac4c85138/OceanDNA-b15082.fa --refList OceanDNA-b15082/target_genomes_gtdb.txt --output OceanDNA-b15082/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:14:48,943] [INFO] Task succeeded: fastANI
[2023-03-14 12:14:48,946] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:14:48,946] [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_014239685.1	s__GCA-2730555 sp014239685	89.1058	379	541	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730555.1	s__GCA-2730555 sp002730555	79.4922	348	541	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.68	99.68	0.93	0.93	2	-
GCA_018650185.1	s__GCA-2730555 sp018650185	78.2974	254	541	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.67	99.66	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2023-03-14 12:14:48,947] [INFO] GTDB search result was written to OceanDNA-b15082/result_gtdb.tsv
[2023-03-14 12:14:48,948] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:14:48,950] [INFO] DFAST_QC result json was written to OceanDNA-b15082/dqc_result.json
[2023-03-14 12:14:48,950] [INFO] DFAST_QC completed!
[2023-03-14 12:14:48,950] [INFO] Total running time: 0h1m6s