[2023-03-19 00:01:03,390] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,390] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg317c687b-8322-41cf-887c-c895dde2e807/dqc_reference
[2023-03-19 00:01:04,514] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,514] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,514] [INFO] Running command: cat /var/lib/cwl/stg78dd45b4-68a0-4d11-a7fa-fac582f27d6c/OceanDNA-b14492.fa | prodigal -d OceanDNA-b14492/cds.fna -a OceanDNA-b14492/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:11,424] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:11,424] [INFO] Task started: HMMsearch
[2023-03-19 00:01:11,424] [INFO] Running command: hmmsearch --tblout OceanDNA-b14492/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg317c687b-8322-41cf-887c-c895dde2e807/dqc_reference/reference_markers.hmm OceanDNA-b14492/protein.faa > /dev/null
[2023-03-19 00:01:11,619] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:11,620] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg78dd45b4-68a0-4d11-a7fa-fac582f27d6c/OceanDNA-b14492.fa]
[2023-03-19 00:01:11,633] [INFO] Query marker FASTA was written to OceanDNA-b14492/markers.fasta
[2023-03-19 00:01:11,633] [INFO] Task started: Blastn
[2023-03-19 00:01:11,633] [INFO] Running command: blastn -query OceanDNA-b14492/markers.fasta -db /var/lib/cwl/stg317c687b-8322-41cf-887c-c895dde2e807/dqc_reference/reference_markers.fasta -out OceanDNA-b14492/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:12,158] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:12,159] [INFO] Selected 12 target genomes.
[2023-03-19 00:01:12,159] [INFO] Target genome list was writen to OceanDNA-b14492/target_genomes.txt
[2023-03-19 00:01:12,165] [INFO] Task started: fastANI
[2023-03-19 00:01:12,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg78dd45b4-68a0-4d11-a7fa-fac582f27d6c/OceanDNA-b14492.fa --refList OceanDNA-b14492/target_genomes.txt --output OceanDNA-b14492/fastani_result.tsv --threads 1
[2023-03-19 00:01:18,027] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:18,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg317c687b-8322-41cf-887c-c895dde2e807/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:18,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg317c687b-8322-41cf-887c-c895dde2e807/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:18,028] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:18,028] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:01:18,028] [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
--------------------------------------------------------------------------------
[2023-03-19 00:01:18,028] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14492/tc_result.tsv
[2023-03-19 00:01:18,028] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:18,028] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:18,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg317c687b-8322-41cf-887c-c895dde2e807/dqc_reference/checkm_data
[2023-03-19 00:01:18,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:18,034] [INFO] Task started: CheckM
[2023-03-19 00:01:18,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14492/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14492/checkm_input OceanDNA-b14492/checkm_result
[2023-03-19 00:01:41,529] [INFO] Task succeeded: CheckM
[2023-03-19 00:01:41,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.91%
Contamintation: 6.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:01:41,531] [INFO] ===== Completeness check finished =====
[2023-03-19 00:01:41,531] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:01:41,531] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14492/markers.fasta)
[2023-03-19 00:01:41,532] [INFO] Task started: Blastn
[2023-03-19 00:01:41,532] [INFO] Running command: blastn -query OceanDNA-b14492/markers.fasta -db /var/lib/cwl/stg317c687b-8322-41cf-887c-c895dde2e807/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14492/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:42,222] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:42,223] [INFO] Selected 9 target genomes.
[2023-03-19 00:01:42,223] [INFO] Target genome list was writen to OceanDNA-b14492/target_genomes_gtdb.txt
[2023-03-19 00:01:42,237] [INFO] Task started: fastANI
[2023-03-19 00:01:42,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg78dd45b4-68a0-4d11-a7fa-fac582f27d6c/OceanDNA-b14492.fa --refList OceanDNA-b14492/target_genomes_gtdb.txt --output OceanDNA-b14492/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:01:45,521] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:45,525] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:01:45,525] [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_008373165.1	s__GCA-002725925 sp009392785	98.7924	313	348	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	98.70	97.00	0.83	0.72	6	conclusive
GCA_002687335.1	s__GCA-002725925 sp002687335	89.9747	183	348	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392215.1	s__GCA-002725925 sp009392215	89.9275	277	348	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725925.1	s__GCA-002725925 sp002725925	83.2444	226	348	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:01:45,525] [INFO] GTDB search result was written to OceanDNA-b14492/result_gtdb.tsv
[2023-03-19 00:01:45,531] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:01:45,531] [INFO] DFAST_QC result json was written to OceanDNA-b14492/dqc_result.json
[2023-03-19 00:01:45,531] [INFO] DFAST_QC completed!
[2023-03-19 00:01:45,531] [INFO] Total running time: 0h0m42s