[2023-03-15 10:21:46,236] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:21:46,238] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:21:46,238] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c29edcb-789a-45a8-9157-ad36c7324ee1/dqc_reference
[2023-03-15 10:21:47,932] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:21:47,933] [INFO] Task started: Prodigal
[2023-03-15 10:21:47,933] [INFO] Running command: cat /var/lib/cwl/stgb692985d-a458-4980-959a-aa6c9d1369f8/OceanDNA-b44532.fa | prodigal -d OceanDNA-b44532/cds.fna -a OceanDNA-b44532/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:21:56,573] [INFO] Task succeeded: Prodigal
[2023-03-15 10:21:56,574] [INFO] Task started: HMMsearch
[2023-03-15 10:21:56,574] [INFO] Running command: hmmsearch --tblout OceanDNA-b44532/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c29edcb-789a-45a8-9157-ad36c7324ee1/dqc_reference/reference_markers.hmm OceanDNA-b44532/protein.faa > /dev/null
[2023-03-15 10:21:56,762] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:21:56,763] [INFO] Found 6/6 markers.
[2023-03-15 10:21:56,773] [INFO] Query marker FASTA was written to OceanDNA-b44532/markers.fasta
[2023-03-15 10:21:56,774] [INFO] Task started: Blastn
[2023-03-15 10:21:56,774] [INFO] Running command: blastn -query OceanDNA-b44532/markers.fasta -db /var/lib/cwl/stg6c29edcb-789a-45a8-9157-ad36c7324ee1/dqc_reference/reference_markers.fasta -out OceanDNA-b44532/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:21:57,330] [INFO] Task succeeded: Blastn
[2023-03-15 10:21:57,331] [INFO] Selected 23 target genomes.
[2023-03-15 10:21:57,331] [INFO] Target genome list was writen to OceanDNA-b44532/target_genomes.txt
[2023-03-15 10:21:57,341] [INFO] Task started: fastANI
[2023-03-15 10:21:57,342] [INFO] Running command: fastANI --query /var/lib/cwl/stgb692985d-a458-4980-959a-aa6c9d1369f8/OceanDNA-b44532.fa --refList OceanDNA-b44532/target_genomes.txt --output OceanDNA-b44532/fastani_result.tsv --threads 1
[2023-03-15 10:22:11,536] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:11,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c29edcb-789a-45a8-9157-ad36c7324ee1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:22:11,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c29edcb-789a-45a8-9157-ad36c7324ee1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:22:11,537] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:22:11,537] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:22:11,537] [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 10:22:11,537] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44532/tc_result.tsv
[2023-03-15 10:22:11,537] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:22:11,537] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:22:11,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c29edcb-789a-45a8-9157-ad36c7324ee1/dqc_reference/checkm_data
[2023-03-15 10:22:11,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:22:11,544] [INFO] Task started: CheckM
[2023-03-15 10:22:11,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44532/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44532/checkm_input OceanDNA-b44532/checkm_result
[2023-03-15 10:22:37,770] [INFO] Task succeeded: CheckM
[2023-03-15 10:22:37,771] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:22:37,773] [INFO] ===== Completeness check finished =====
[2023-03-15 10:22:37,773] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:22:37,773] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44532/markers.fasta)
[2023-03-15 10:22:37,773] [INFO] Task started: Blastn
[2023-03-15 10:22:37,773] [INFO] Running command: blastn -query OceanDNA-b44532/markers.fasta -db /var/lib/cwl/stg6c29edcb-789a-45a8-9157-ad36c7324ee1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44532/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:38,731] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:38,732] [INFO] Selected 20 target genomes.
[2023-03-15 10:22:38,732] [INFO] Target genome list was writen to OceanDNA-b44532/target_genomes_gtdb.txt
[2023-03-15 10:22:39,498] [INFO] Task started: fastANI
[2023-03-15 10:22:39,498] [INFO] Running command: fastANI --query /var/lib/cwl/stgb692985d-a458-4980-959a-aa6c9d1369f8/OceanDNA-b44532.fa --refList OceanDNA-b44532/target_genomes_gtdb.txt --output OceanDNA-b44532/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:22:46,609] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:46,612] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:22:46,612] [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_002715745.1	s__SP4260 sp002715745	97.8179	400	520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	97.07	97.07	0.87	0.87	2	conclusive
GCA_902517795.1	s__SP4260 sp902517795	89.9217	302	520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	99.80	99.80	0.68	0.68	2	-
GCA_002728725.1	s__SP4260 sp002728725	89.1791	305	520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331585.1	s__SP4260 sp003331585	78.2815	89	520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:22:46,613] [INFO] GTDB search result was written to OceanDNA-b44532/result_gtdb.tsv
[2023-03-15 10:22:46,613] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:22:46,613] [INFO] DFAST_QC result json was written to OceanDNA-b44532/dqc_result.json
[2023-03-15 10:22:46,613] [INFO] DFAST_QC completed!
[2023-03-15 10:22:46,613] [INFO] Total running time: 0h1m0s