[2023-03-19 00:15:41,728] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,728] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,728] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7b71d68-be3f-4e7a-a110-38cd7baf9d74/dqc_reference
[2023-03-19 00:15:43,438] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,439] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,439] [INFO] Running command: cat /var/lib/cwl/stg06840472-ec3f-4301-85f9-ee4340e04ca9/OceanDNA-b32699.fa | prodigal -d OceanDNA-b32699/cds.fna -a OceanDNA-b32699/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:16:06,603] [INFO] Task succeeded: Prodigal
[2023-03-19 00:16:06,603] [INFO] Task started: HMMsearch
[2023-03-19 00:16:06,603] [INFO] Running command: hmmsearch --tblout OceanDNA-b32699/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7b71d68-be3f-4e7a-a110-38cd7baf9d74/dqc_reference/reference_markers.hmm OceanDNA-b32699/protein.faa > /dev/null
[2023-03-19 00:16:06,862] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:16:06,863] [INFO] Found 6/6 markers.
[2023-03-19 00:16:06,895] [INFO] Query marker FASTA was written to OceanDNA-b32699/markers.fasta
[2023-03-19 00:16:06,897] [INFO] Task started: Blastn
[2023-03-19 00:16:06,897] [INFO] Running command: blastn -query OceanDNA-b32699/markers.fasta -db /var/lib/cwl/stgb7b71d68-be3f-4e7a-a110-38cd7baf9d74/dqc_reference/reference_markers.fasta -out OceanDNA-b32699/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:07,478] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:07,479] [INFO] Selected 25 target genomes.
[2023-03-19 00:16:07,479] [INFO] Target genome list was writen to OceanDNA-b32699/target_genomes.txt
[2023-03-19 00:16:07,502] [INFO] Task started: fastANI
[2023-03-19 00:16:07,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg06840472-ec3f-4301-85f9-ee4340e04ca9/OceanDNA-b32699.fa --refList OceanDNA-b32699/target_genomes.txt --output OceanDNA-b32699/fastani_result.tsv --threads 1
[2023-03-19 00:16:27,327] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:27,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7b71d68-be3f-4e7a-a110-38cd7baf9d74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:27,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7b71d68-be3f-4e7a-a110-38cd7baf9d74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:27,331] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:27,331] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:16:27,331] [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
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.3008	51	1212	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:27,332] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32699/tc_result.tsv
[2023-03-19 00:16:27,332] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:27,332] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:27,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7b71d68-be3f-4e7a-a110-38cd7baf9d74/dqc_reference/checkm_data
[2023-03-19 00:16:27,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:27,339] [INFO] Task started: CheckM
[2023-03-19 00:16:27,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32699/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32699/checkm_input OceanDNA-b32699/checkm_result
[2023-03-19 00:17:26,198] [INFO] Task succeeded: CheckM
[2023-03-19 00:17:26,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:17:26,201] [INFO] ===== Completeness check finished =====
[2023-03-19 00:17:26,201] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:17:26,201] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32699/markers.fasta)
[2023-03-19 00:17:26,203] [INFO] Task started: Blastn
[2023-03-19 00:17:26,203] [INFO] Running command: blastn -query OceanDNA-b32699/markers.fasta -db /var/lib/cwl/stgb7b71d68-be3f-4e7a-a110-38cd7baf9d74/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32699/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:17:27,114] [INFO] Task succeeded: Blastn
[2023-03-19 00:17:27,116] [INFO] Selected 29 target genomes.
[2023-03-19 00:17:27,116] [INFO] Target genome list was writen to OceanDNA-b32699/target_genomes_gtdb.txt
[2023-03-19 00:17:27,140] [INFO] Task started: fastANI
[2023-03-19 00:17:27,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg06840472-ec3f-4301-85f9-ee4340e04ca9/OceanDNA-b32699.fa --refList OceanDNA-b32699/target_genomes_gtdb.txt --output OceanDNA-b32699/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:17:46,910] [INFO] Task succeeded: fastANI
[2023-03-19 00:17:46,912] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:17:46,912] [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_002348365.1	s__UBA2966 sp002348365	99.3299	1090	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__UBA2966	95.0	98.52	97.79	0.84	0.83	3	conclusive
--------------------------------------------------------------------------------
[2023-03-19 00:17:46,912] [INFO] GTDB search result was written to OceanDNA-b32699/result_gtdb.tsv
[2023-03-19 00:17:46,913] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:17:46,913] [INFO] DFAST_QC result json was written to OceanDNA-b32699/dqc_result.json
[2023-03-19 00:17:46,913] [INFO] DFAST_QC completed!
[2023-03-19 00:17:46,914] [INFO] Total running time: 0h2m5s