[2023-03-15 09:48:16,398] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,398] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,399] [INFO] DQC Reference Directory: /var/lib/cwl/stgaee18f22-309e-49bf-9483-e69e0c1d60c0/dqc_reference
[2023-03-15 09:48:18,053] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,054] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,054] [INFO] Running command: cat /var/lib/cwl/stgf2a25893-e3be-4ebb-b2fb-76bf472fa0e0/OceanDNA-b19325.fa | prodigal -d OceanDNA-b19325/cds.fna -a OceanDNA-b19325/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:24,358] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:24,358] [INFO] Task started: HMMsearch
[2023-03-15 09:48:24,358] [INFO] Running command: hmmsearch --tblout OceanDNA-b19325/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaee18f22-309e-49bf-9483-e69e0c1d60c0/dqc_reference/reference_markers.hmm OceanDNA-b19325/protein.faa > /dev/null
[2023-03-15 09:48:24,524] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:24,525] [INFO] Found 6/6 markers.
[2023-03-15 09:48:24,536] [INFO] Query marker FASTA was written to OceanDNA-b19325/markers.fasta
[2023-03-15 09:48:24,536] [INFO] Task started: Blastn
[2023-03-15 09:48:24,536] [INFO] Running command: blastn -query OceanDNA-b19325/markers.fasta -db /var/lib/cwl/stgaee18f22-309e-49bf-9483-e69e0c1d60c0/dqc_reference/reference_markers.fasta -out OceanDNA-b19325/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:25,076] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:25,077] [INFO] Selected 26 target genomes.
[2023-03-15 09:48:25,077] [INFO] Target genome list was writen to OceanDNA-b19325/target_genomes.txt
[2023-03-15 09:48:25,099] [INFO] Task started: fastANI
[2023-03-15 09:48:25,099] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2a25893-e3be-4ebb-b2fb-76bf472fa0e0/OceanDNA-b19325.fa --refList OceanDNA-b19325/target_genomes.txt --output OceanDNA-b19325/fastani_result.tsv --threads 1
[2023-03-15 09:48:34,997] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:34,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaee18f22-309e-49bf-9483-e69e0c1d60c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:34,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaee18f22-309e-49bf-9483-e69e0c1d60c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:34,998] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:34,998] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:34,998] [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 09:48:34,998] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19325/tc_result.tsv
[2023-03-15 09:48:34,998] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:34,998] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:34,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaee18f22-309e-49bf-9483-e69e0c1d60c0/dqc_reference/checkm_data
[2023-03-15 09:48:35,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:35,004] [INFO] Task started: CheckM
[2023-03-15 09:48:35,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19325/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19325/checkm_input OceanDNA-b19325/checkm_result
[2023-03-15 09:48:56,411] [INFO] Task succeeded: CheckM
[2023-03-15 09:48:56,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:48:56,413] [INFO] ===== Completeness check finished =====
[2023-03-15 09:48:56,413] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:48:56,413] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19325/markers.fasta)
[2023-03-15 09:48:56,413] [INFO] Task started: Blastn
[2023-03-15 09:48:56,413] [INFO] Running command: blastn -query OceanDNA-b19325/markers.fasta -db /var/lib/cwl/stgaee18f22-309e-49bf-9483-e69e0c1d60c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19325/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:57,203] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:57,204] [INFO] Selected 34 target genomes.
[2023-03-15 09:48:57,205] [INFO] Target genome list was writen to OceanDNA-b19325/target_genomes_gtdb.txt
[2023-03-15 09:48:57,993] [INFO] Task started: fastANI
[2023-03-15 09:48:57,993] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2a25893-e3be-4ebb-b2fb-76bf472fa0e0/OceanDNA-b19325.fa --refList OceanDNA-b19325/target_genomes_gtdb.txt --output OceanDNA-b19325/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:09,434] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:09,438] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:49:09,438] [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_002172545.1	s__TMED108 sp002172545	80.7695	212	392	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	99.45	99.45	0.75	0.75	2	-
GCA_002724735.1	s__TMED108 sp002724735	77.412	80	392	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717765.1	s__TMED108 sp002717765	77.2817	96	392	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712245.1	s__TMED108 sp002712245	77.0752	70	392	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:09,438] [INFO] GTDB search result was written to OceanDNA-b19325/result_gtdb.tsv
[2023-03-15 09:49:09,438] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:09,439] [INFO] DFAST_QC result json was written to OceanDNA-b19325/dqc_result.json
[2023-03-15 09:49:09,439] [INFO] DFAST_QC completed!
[2023-03-15 09:49:09,439] [INFO] Total running time: 0h0m53s