[2023-03-17 10:35:02,807] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:35:02,808] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:35:02,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c773e4b-7237-4ed3-80b8-1017c60ca162/dqc_reference
[2023-03-17 10:35:04,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:35:04,550] [INFO] Task started: Prodigal
[2023-03-17 10:35:04,550] [INFO] Running command: cat /var/lib/cwl/stg9772c715-e2f0-4c44-9276-d800d9c6f3e9/OceanDNA-b33529.fa | prodigal -d OceanDNA-b33529/cds.fna -a OceanDNA-b33529/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:35:11,382] [INFO] Task succeeded: Prodigal
[2023-03-17 10:35:11,382] [INFO] Task started: HMMsearch
[2023-03-17 10:35:11,382] [INFO] Running command: hmmsearch --tblout OceanDNA-b33529/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c773e4b-7237-4ed3-80b8-1017c60ca162/dqc_reference/reference_markers.hmm OceanDNA-b33529/protein.faa > /dev/null
[2023-03-17 10:35:11,528] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:35:11,529] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9772c715-e2f0-4c44-9276-d800d9c6f3e9/OceanDNA-b33529.fa]
[2023-03-17 10:35:11,543] [INFO] Query marker FASTA was written to OceanDNA-b33529/markers.fasta
[2023-03-17 10:35:11,543] [INFO] Task started: Blastn
[2023-03-17 10:35:11,543] [INFO] Running command: blastn -query OceanDNA-b33529/markers.fasta -db /var/lib/cwl/stg9c773e4b-7237-4ed3-80b8-1017c60ca162/dqc_reference/reference_markers.fasta -out OceanDNA-b33529/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:12,101] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:12,102] [INFO] Selected 15 target genomes.
[2023-03-17 10:35:12,102] [INFO] Target genome list was writen to OceanDNA-b33529/target_genomes.txt
[2023-03-17 10:35:12,111] [INFO] Task started: fastANI
[2023-03-17 10:35:12,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg9772c715-e2f0-4c44-9276-d800d9c6f3e9/OceanDNA-b33529.fa --refList OceanDNA-b33529/target_genomes.txt --output OceanDNA-b33529/fastani_result.tsv --threads 1
[2023-03-17 10:35:22,680] [INFO] Task succeeded: fastANI
[2023-03-17 10:35:22,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c773e4b-7237-4ed3-80b8-1017c60ca162/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:35:22,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c773e4b-7237-4ed3-80b8-1017c60ca162/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:35:22,684] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:35:22,684] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:35:22,684] [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
Zwartia hollandica	strain=LF4-65	GCA_019923725.1	324606	324606	type	True	77.328	63	324	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:35:22,684] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33529/tc_result.tsv
[2023-03-17 10:35:22,684] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:35:22,685] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:35:22,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c773e4b-7237-4ed3-80b8-1017c60ca162/dqc_reference/checkm_data
[2023-03-17 10:35:22,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:35:22,699] [INFO] Task started: CheckM
[2023-03-17 10:35:22,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33529/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33529/checkm_input OceanDNA-b33529/checkm_result
[2023-03-17 10:35:45,586] [INFO] Task succeeded: CheckM
[2023-03-17 10:35:45,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:35:45,588] [INFO] ===== Completeness check finished =====
[2023-03-17 10:35:45,589] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:35:45,589] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33529/markers.fasta)
[2023-03-17 10:35:45,590] [INFO] Task started: Blastn
[2023-03-17 10:35:45,590] [INFO] Running command: blastn -query OceanDNA-b33529/markers.fasta -db /var/lib/cwl/stg9c773e4b-7237-4ed3-80b8-1017c60ca162/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33529/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:46,373] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:46,374] [INFO] Selected 18 target genomes.
[2023-03-17 10:35:46,374] [INFO] Target genome list was writen to OceanDNA-b33529/target_genomes_gtdb.txt
[2023-03-17 10:35:46,721] [INFO] Task started: fastANI
[2023-03-17 10:35:46,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg9772c715-e2f0-4c44-9276-d800d9c6f3e9/OceanDNA-b33529.fa --refList OceanDNA-b33529/target_genomes_gtdb.txt --output OceanDNA-b33529/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:35:56,601] [INFO] Task succeeded: fastANI
[2023-03-17 10:35:56,604] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:35:56,604] [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_002292845.1	s__NBD-18 sp002292845	79.5071	171	324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958565.1	s__NBD-18 sp903958565	77.4559	56	324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.16	98.92	0.86	0.85	5	-
GCA_903847325.1	s__NBD-18 sp903847325	76.7867	56	324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:35:56,604] [INFO] GTDB search result was written to OceanDNA-b33529/result_gtdb.tsv
[2023-03-17 10:35:56,604] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:35:56,605] [INFO] DFAST_QC result json was written to OceanDNA-b33529/dqc_result.json
[2023-03-17 10:35:56,605] [INFO] DFAST_QC completed!
[2023-03-17 10:35:56,605] [INFO] Total running time: 0h0m54s