[2023-03-15 04:04:36,568] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:04:36,568] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:04:36,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e83de02-e908-4198-97b6-57807cde932c/dqc_reference
[2023-03-15 04:04:39,814] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:04:39,815] [INFO] Task started: Prodigal
[2023-03-15 04:04:39,815] [INFO] Running command: cat /var/lib/cwl/stg3efb2055-9ace-470a-9099-0019ae473215/OceanDNA-b21712.fa | prodigal -d OceanDNA-b21712/cds.fna -a OceanDNA-b21712/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:04:43,200] [INFO] Task succeeded: Prodigal
[2023-03-15 04:04:43,200] [INFO] Task started: HMMsearch
[2023-03-15 04:04:43,200] [INFO] Running command: hmmsearch --tblout OceanDNA-b21712/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e83de02-e908-4198-97b6-57807cde932c/dqc_reference/reference_markers.hmm OceanDNA-b21712/protein.faa > /dev/null
[2023-03-15 04:04:43,405] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:04:43,406] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3efb2055-9ace-470a-9099-0019ae473215/OceanDNA-b21712.fa]
[2023-03-15 04:04:43,411] [INFO] Query marker FASTA was written to OceanDNA-b21712/markers.fasta
[2023-03-15 04:04:43,413] [INFO] Task started: Blastn
[2023-03-15 04:04:43,413] [INFO] Running command: blastn -query OceanDNA-b21712/markers.fasta -db /var/lib/cwl/stg8e83de02-e908-4198-97b6-57807cde932c/dqc_reference/reference_markers.fasta -out OceanDNA-b21712/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:04:47,485] [INFO] Task succeeded: Blastn
[2023-03-15 04:04:47,486] [INFO] Selected 10 target genomes.
[2023-03-15 04:04:47,487] [INFO] Target genome list was writen to OceanDNA-b21712/target_genomes.txt
[2023-03-15 04:04:47,493] [INFO] Task started: fastANI
[2023-03-15 04:04:47,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg3efb2055-9ace-470a-9099-0019ae473215/OceanDNA-b21712.fa --refList OceanDNA-b21712/target_genomes.txt --output OceanDNA-b21712/fastani_result.tsv --threads 1
[2023-03-15 04:04:53,745] [INFO] Task succeeded: fastANI
[2023-03-15 04:04:53,746] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e83de02-e908-4198-97b6-57807cde932c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:04:53,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e83de02-e908-4198-97b6-57807cde932c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:04:53,746] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:04:53,746] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:04:53,746] [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
--------------------------------------------------------------------------------
[2023-03-15 04:04:53,747] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21712/tc_result.tsv
[2023-03-15 04:04:53,747] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:04:53,747] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:04:53,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e83de02-e908-4198-97b6-57807cde932c/dqc_reference/checkm_data
[2023-03-15 04:04:53,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:04:53,756] [INFO] Task started: CheckM
[2023-03-15 04:04:53,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21712/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21712/checkm_input OceanDNA-b21712/checkm_result
[2023-03-15 04:05:10,232] [INFO] Task succeeded: CheckM
[2023-03-15 04:05:10,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:05:10,262] [INFO] ===== Completeness check finished =====
[2023-03-15 04:05:10,263] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:05:10,263] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21712/markers.fasta)
[2023-03-15 04:05:10,264] [INFO] Task started: Blastn
[2023-03-15 04:05:10,265] [INFO] Running command: blastn -query OceanDNA-b21712/markers.fasta -db /var/lib/cwl/stg8e83de02-e908-4198-97b6-57807cde932c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21712/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:05:11,248] [INFO] Task succeeded: Blastn
[2023-03-15 04:05:11,253] [INFO] Selected 15 target genomes.
[2023-03-15 04:05:11,253] [INFO] Target genome list was writen to OceanDNA-b21712/target_genomes_gtdb.txt
[2023-03-15 04:05:11,293] [INFO] Task started: fastANI
[2023-03-15 04:05:11,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg3efb2055-9ace-470a-9099-0019ae473215/OceanDNA-b21712.fa --refList OceanDNA-b21712/target_genomes_gtdb.txt --output OceanDNA-b21712/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:05:17,308] [INFO] Task succeeded: fastANI
[2023-03-15 04:05:17,310] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:05:17,310] [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_002685955.1	s__UBA2143 sp002685955	99.9289	117	177	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Portnoybacterales;f__UBA2143;g__UBA2143	95.0	99.90	99.90	0.71	0.71	2	conclusive
--------------------------------------------------------------------------------
[2023-03-15 04:05:17,312] [INFO] GTDB search result was written to OceanDNA-b21712/result_gtdb.tsv
[2023-03-15 04:05:17,314] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:05:17,317] [INFO] DFAST_QC result json was written to OceanDNA-b21712/dqc_result.json
[2023-03-15 04:05:17,317] [INFO] DFAST_QC completed!
[2023-03-15 04:05:17,317] [INFO] Total running time: 0h0m41s