[2023-03-17 23:08:31,972] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,973] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,973] [INFO] DQC Reference Directory: /var/lib/cwl/stg5668a2b0-7836-4171-8dca-92408d8b2447/dqc_reference
[2023-03-17 23:08:33,170] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,171] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,171] [INFO] Running command: cat /var/lib/cwl/stg47bb417f-cda5-4e05-af7c-9d0fa10e5115/OceanDNA-b40263.fa | prodigal -d OceanDNA-b40263/cds.fna -a OceanDNA-b40263/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:08:39,303] [INFO] Task succeeded: Prodigal
[2023-03-17 23:08:39,303] [INFO] Task started: HMMsearch
[2023-03-17 23:08:39,304] [INFO] Running command: hmmsearch --tblout OceanDNA-b40263/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5668a2b0-7836-4171-8dca-92408d8b2447/dqc_reference/reference_markers.hmm OceanDNA-b40263/protein.faa > /dev/null
[2023-03-17 23:08:39,482] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:08:39,483] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg47bb417f-cda5-4e05-af7c-9d0fa10e5115/OceanDNA-b40263.fa]
[2023-03-17 23:08:39,500] [INFO] Query marker FASTA was written to OceanDNA-b40263/markers.fasta
[2023-03-17 23:08:39,500] [INFO] Task started: Blastn
[2023-03-17 23:08:39,501] [INFO] Running command: blastn -query OceanDNA-b40263/markers.fasta -db /var/lib/cwl/stg5668a2b0-7836-4171-8dca-92408d8b2447/dqc_reference/reference_markers.fasta -out OceanDNA-b40263/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:08:39,951] [INFO] Task succeeded: Blastn
[2023-03-17 23:08:39,952] [INFO] Selected 20 target genomes.
[2023-03-17 23:08:39,952] [INFO] Target genome list was writen to OceanDNA-b40263/target_genomes.txt
[2023-03-17 23:08:39,964] [INFO] Task started: fastANI
[2023-03-17 23:08:39,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg47bb417f-cda5-4e05-af7c-9d0fa10e5115/OceanDNA-b40263.fa --refList OceanDNA-b40263/target_genomes.txt --output OceanDNA-b40263/fastani_result.tsv --threads 1
[2023-03-17 23:08:51,542] [INFO] Task succeeded: fastANI
[2023-03-17 23:08:51,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5668a2b0-7836-4171-8dca-92408d8b2447/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:08:51,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5668a2b0-7836-4171-8dca-92408d8b2447/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:08:51,542] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:08:51,543] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:08:51,543] [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 23:08:51,543] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40263/tc_result.tsv
[2023-03-17 23:08:51,543] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:08:51,543] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:08:51,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5668a2b0-7836-4171-8dca-92408d8b2447/dqc_reference/checkm_data
[2023-03-17 23:08:51,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:08:51,567] [INFO] Task started: CheckM
[2023-03-17 23:08:51,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40263/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40263/checkm_input OceanDNA-b40263/checkm_result
[2023-03-17 23:09:13,827] [INFO] Task succeeded: CheckM
[2023-03-17 23:09:13,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 6.71%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-17 23:09:13,835] [INFO] ===== Completeness check finished =====
[2023-03-17 23:09:13,835] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:09:13,835] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40263/markers.fasta)
[2023-03-17 23:09:13,836] [INFO] Task started: Blastn
[2023-03-17 23:09:13,836] [INFO] Running command: blastn -query OceanDNA-b40263/markers.fasta -db /var/lib/cwl/stg5668a2b0-7836-4171-8dca-92408d8b2447/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40263/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:14,328] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:14,330] [INFO] Selected 16 target genomes.
[2023-03-17 23:09:14,330] [INFO] Target genome list was writen to OceanDNA-b40263/target_genomes_gtdb.txt
[2023-03-17 23:09:14,341] [INFO] Task started: fastANI
[2023-03-17 23:09:14,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg47bb417f-cda5-4e05-af7c-9d0fa10e5115/OceanDNA-b40263.fa --refList OceanDNA-b40263/target_genomes_gtdb.txt --output OceanDNA-b40263/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:09:23,547] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:23,550] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:09:23,551] [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_001438145.1	s__UBA9145 sp001438145	92.0054	214	252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.16	96.74	0.82	0.76	25	-
GCA_018401885.1	s__UBA9145 sp018401885	79.3343	170	252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.27	98.07	0.94	0.93	3	-
GCA_017853205.1	s__UBA9145 sp003482475	79.0724	169	252	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.11	98.58	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2023-03-17 23:09:23,552] [INFO] GTDB search result was written to OceanDNA-b40263/result_gtdb.tsv
[2023-03-17 23:09:23,553] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:09:23,555] [INFO] DFAST_QC result json was written to OceanDNA-b40263/dqc_result.json
[2023-03-17 23:09:23,556] [INFO] DFAST_QC completed!
[2023-03-17 23:09:23,556] [INFO] Total running time: 0h0m52s