[2023-03-14 14:44:33,140] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:44:33,140] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:44:33,140] [INFO] DQC Reference Directory: /var/lib/cwl/stg1296db98-b00c-4e8b-bdfc-f75d02ed7f5d/dqc_reference
[2023-03-14 14:44:34,519] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:44:34,519] [INFO] Task started: Prodigal
[2023-03-14 14:44:34,520] [INFO] Running command: cat /var/lib/cwl/stga286eea8-9d24-493f-9f86-dee557346fcd/OceanDNA-b45303.fa | prodigal -d OceanDNA-b45303/cds.fna -a OceanDNA-b45303/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:44:39,213] [INFO] Task succeeded: Prodigal
[2023-03-14 14:44:39,213] [INFO] Task started: HMMsearch
[2023-03-14 14:44:39,213] [INFO] Running command: hmmsearch --tblout OceanDNA-b45303/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1296db98-b00c-4e8b-bdfc-f75d02ed7f5d/dqc_reference/reference_markers.hmm OceanDNA-b45303/protein.faa > /dev/null
[2023-03-14 14:44:39,420] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:44:39,421] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga286eea8-9d24-493f-9f86-dee557346fcd/OceanDNA-b45303.fa]
[2023-03-14 14:44:39,433] [INFO] Query marker FASTA was written to OceanDNA-b45303/markers.fasta
[2023-03-14 14:44:39,435] [INFO] Task started: Blastn
[2023-03-14 14:44:39,435] [INFO] Running command: blastn -query OceanDNA-b45303/markers.fasta -db /var/lib/cwl/stg1296db98-b00c-4e8b-bdfc-f75d02ed7f5d/dqc_reference/reference_markers.fasta -out OceanDNA-b45303/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:44:40,204] [INFO] Task succeeded: Blastn
[2023-03-14 14:44:40,204] [INFO] Selected 5 target genomes.
[2023-03-14 14:44:40,205] [INFO] Target genome list was writen to OceanDNA-b45303/target_genomes.txt
[2023-03-14 14:44:40,208] [INFO] Task started: fastANI
[2023-03-14 14:44:40,208] [INFO] Running command: fastANI --query /var/lib/cwl/stga286eea8-9d24-493f-9f86-dee557346fcd/OceanDNA-b45303.fa --refList OceanDNA-b45303/target_genomes.txt --output OceanDNA-b45303/fastani_result.tsv --threads 1
[2023-03-14 14:44:43,411] [INFO] Task succeeded: fastANI
[2023-03-14 14:44:43,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1296db98-b00c-4e8b-bdfc-f75d02ed7f5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:44:43,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1296db98-b00c-4e8b-bdfc-f75d02ed7f5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:44:43,412] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:44:43,412] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:44:43,412] [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 14:44:43,412] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45303/tc_result.tsv
[2023-03-14 14:44:43,412] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:44:43,412] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:44:43,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1296db98-b00c-4e8b-bdfc-f75d02ed7f5d/dqc_reference/checkm_data
[2023-03-14 14:44:43,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:44:43,418] [INFO] Task started: CheckM
[2023-03-14 14:44:43,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45303/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45303/checkm_input OceanDNA-b45303/checkm_result
[2023-03-14 14:45:06,053] [INFO] Task succeeded: CheckM
[2023-03-14 14:45:06,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 14:45:06,055] [INFO] ===== Completeness check finished =====
[2023-03-14 14:45:06,055] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:45:06,055] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45303/markers.fasta)
[2023-03-14 14:45:06,057] [INFO] Task started: Blastn
[2023-03-14 14:45:06,057] [INFO] Running command: blastn -query OceanDNA-b45303/markers.fasta -db /var/lib/cwl/stg1296db98-b00c-4e8b-bdfc-f75d02ed7f5d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45303/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:45:06,984] [INFO] Task succeeded: Blastn
[2023-03-14 14:45:06,985] [INFO] Selected 12 target genomes.
[2023-03-14 14:45:06,985] [INFO] Target genome list was writen to OceanDNA-b45303/target_genomes_gtdb.txt
[2023-03-14 14:45:07,068] [INFO] Task started: fastANI
[2023-03-14 14:45:07,068] [INFO] Running command: fastANI --query /var/lib/cwl/stga286eea8-9d24-493f-9f86-dee557346fcd/OceanDNA-b45303.fa --refList OceanDNA-b45303/target_genomes_gtdb.txt --output OceanDNA-b45303/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:45:10,820] [INFO] Task succeeded: fastANI
[2023-03-14 14:45:10,822] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:45:10,823] [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_002501535.1	s__UBA6624 sp002501535	90.7784	202	275	d__Bacteria;p__UBP7;c__UBA6624;o__UBA6624;f__UBA6624;g__UBA6624	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002716355.1	s__UBA6624 sp002716355	86.8328	261	275	d__Bacteria;p__UBP7;c__UBA6624;o__UBA6624;f__UBA6624;g__UBA6624	95.0	98.83	97.75	0.96	0.95	3	-
--------------------------------------------------------------------------------
[2023-03-14 14:45:10,823] [INFO] GTDB search result was written to OceanDNA-b45303/result_gtdb.tsv
[2023-03-14 14:45:10,823] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:45:10,824] [INFO] DFAST_QC result json was written to OceanDNA-b45303/dqc_result.json
[2023-03-14 14:45:10,824] [INFO] DFAST_QC completed!
[2023-03-14 14:45:10,824] [INFO] Total running time: 0h0m38s