[2023-03-17 11:08:00,267] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,269] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,269] [INFO] DQC Reference Directory: /var/lib/cwl/stg88ff3474-2f6b-48cb-95dd-a583ef225c44/dqc_reference
[2023-03-17 11:08:01,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,419] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,419] [INFO] Running command: cat /var/lib/cwl/stg4e91cfe7-6498-4a75-9255-3f6adefa5ee4/OceanDNA-b44218.fa | prodigal -d OceanDNA-b44218/cds.fna -a OceanDNA-b44218/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:08,978] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:08,978] [INFO] Task started: HMMsearch
[2023-03-17 11:08:08,978] [INFO] Running command: hmmsearch --tblout OceanDNA-b44218/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88ff3474-2f6b-48cb-95dd-a583ef225c44/dqc_reference/reference_markers.hmm OceanDNA-b44218/protein.faa > /dev/null
[2023-03-17 11:08:09,155] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:09,156] [INFO] Found 6/6 markers.
[2023-03-17 11:08:09,196] [INFO] Query marker FASTA was written to OceanDNA-b44218/markers.fasta
[2023-03-17 11:08:09,197] [INFO] Task started: Blastn
[2023-03-17 11:08:09,197] [INFO] Running command: blastn -query OceanDNA-b44218/markers.fasta -db /var/lib/cwl/stg88ff3474-2f6b-48cb-95dd-a583ef225c44/dqc_reference/reference_markers.fasta -out OceanDNA-b44218/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:09,799] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:09,812] [INFO] Selected 31 target genomes.
[2023-03-17 11:08:09,813] [INFO] Target genome list was writen to OceanDNA-b44218/target_genomes.txt
[2023-03-17 11:08:09,829] [INFO] Task started: fastANI
[2023-03-17 11:08:09,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e91cfe7-6498-4a75-9255-3f6adefa5ee4/OceanDNA-b44218.fa --refList OceanDNA-b44218/target_genomes.txt --output OceanDNA-b44218/fastani_result.tsv --threads 1
[2023-03-17 11:08:26,653] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:26,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88ff3474-2f6b-48cb-95dd-a583ef225c44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:26,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88ff3474-2f6b-48cb-95dd-a583ef225c44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:26,654] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:26,654] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:08:26,654] [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 11:08:26,658] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44218/tc_result.tsv
[2023-03-17 11:08:26,663] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:26,664] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:26,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88ff3474-2f6b-48cb-95dd-a583ef225c44/dqc_reference/checkm_data
[2023-03-17 11:08:26,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:26,674] [INFO] Task started: CheckM
[2023-03-17 11:08:26,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44218/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44218/checkm_input OceanDNA-b44218/checkm_result
[2023-03-17 11:08:50,699] [INFO] Task succeeded: CheckM
[2023-03-17 11:08:50,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:08:50,757] [INFO] ===== Completeness check finished =====
[2023-03-17 11:08:50,757] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:08:50,757] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44218/markers.fasta)
[2023-03-17 11:08:50,759] [INFO] Task started: Blastn
[2023-03-17 11:08:50,759] [INFO] Running command: blastn -query OceanDNA-b44218/markers.fasta -db /var/lib/cwl/stg88ff3474-2f6b-48cb-95dd-a583ef225c44/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44218/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:51,731] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:51,900] [INFO] Selected 25 target genomes.
[2023-03-17 11:08:51,900] [INFO] Target genome list was writen to OceanDNA-b44218/target_genomes_gtdb.txt
[2023-03-17 11:08:52,337] [INFO] Task started: fastANI
[2023-03-17 11:08:52,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e91cfe7-6498-4a75-9255-3f6adefa5ee4/OceanDNA-b44218.fa --refList OceanDNA-b44218/target_genomes_gtdb.txt --output OceanDNA-b44218/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:09:04,869] [INFO] Task succeeded: fastANI
[2023-03-17 11:09:04,871] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:09:04,871] [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_002386945.1	s__UBA4575 sp002386945	82.8465	312	457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4575;f__UBA4575;g__UBA4575	95.0	98.70	97.48	0.92	0.88	5	-
GCA_905479295.1	s__UBA4575 sp905479295	82.1168	241	457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4575;f__UBA4575;g__UBA4575	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:09:04,874] [INFO] GTDB search result was written to OceanDNA-b44218/result_gtdb.tsv
[2023-03-17 11:09:04,878] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:09:04,882] [INFO] DFAST_QC result json was written to OceanDNA-b44218/dqc_result.json
[2023-03-17 11:09:04,883] [INFO] DFAST_QC completed!
[2023-03-17 11:09:04,883] [INFO] Total running time: 0h1m5s