[2023-03-17 04:15:14,765] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:14,765] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:14,765] [INFO] DQC Reference Directory: /var/lib/cwl/stgfef4e7e3-bccd-46f6-a8b4-aadcf3f7f2d7/dqc_reference
[2023-03-17 04:15:16,103] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,103] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,104] [INFO] Running command: cat /var/lib/cwl/stgba51b707-e478-4fb5-8df5-c1523ebd3adf/OceanDNA-b26910.fa | prodigal -d OceanDNA-b26910/cds.fna -a OceanDNA-b26910/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:22,990] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:22,991] [INFO] Task started: HMMsearch
[2023-03-17 04:15:22,991] [INFO] Running command: hmmsearch --tblout OceanDNA-b26910/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfef4e7e3-bccd-46f6-a8b4-aadcf3f7f2d7/dqc_reference/reference_markers.hmm OceanDNA-b26910/protein.faa > /dev/null
[2023-03-17 04:15:23,200] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:23,200] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgba51b707-e478-4fb5-8df5-c1523ebd3adf/OceanDNA-b26910.fa]
[2023-03-17 04:15:23,215] [INFO] Query marker FASTA was written to OceanDNA-b26910/markers.fasta
[2023-03-17 04:15:23,216] [INFO] Task started: Blastn
[2023-03-17 04:15:23,216] [INFO] Running command: blastn -query OceanDNA-b26910/markers.fasta -db /var/lib/cwl/stgfef4e7e3-bccd-46f6-a8b4-aadcf3f7f2d7/dqc_reference/reference_markers.fasta -out OceanDNA-b26910/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:23,823] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:23,824] [INFO] Selected 25 target genomes.
[2023-03-17 04:15:23,824] [INFO] Target genome list was writen to OceanDNA-b26910/target_genomes.txt
[2023-03-17 04:15:23,836] [INFO] Task started: fastANI
[2023-03-17 04:15:23,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgba51b707-e478-4fb5-8df5-c1523ebd3adf/OceanDNA-b26910.fa --refList OceanDNA-b26910/target_genomes.txt --output OceanDNA-b26910/fastani_result.tsv --threads 1
[2023-03-17 04:15:42,836] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:42,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfef4e7e3-bccd-46f6-a8b4-aadcf3f7f2d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:42,837] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfef4e7e3-bccd-46f6-a8b4-aadcf3f7f2d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:42,837] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:42,837] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:15:42,837] [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
--------------------------------------------------------------------------------
[2023-03-17 04:15:42,837] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26910/tc_result.tsv
[2023-03-17 04:15:42,837] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:42,837] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:42,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfef4e7e3-bccd-46f6-a8b4-aadcf3f7f2d7/dqc_reference/checkm_data
[2023-03-17 04:15:42,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:42,843] [INFO] Task started: CheckM
[2023-03-17 04:15:42,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26910/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26910/checkm_input OceanDNA-b26910/checkm_result
[2023-03-17 04:16:05,494] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:05,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:05,496] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:05,496] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:05,496] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26910/markers.fasta)
[2023-03-17 04:16:05,497] [INFO] Task started: Blastn
[2023-03-17 04:16:05,497] [INFO] Running command: blastn -query OceanDNA-b26910/markers.fasta -db /var/lib/cwl/stgfef4e7e3-bccd-46f6-a8b4-aadcf3f7f2d7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26910/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:06,398] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:06,399] [INFO] Selected 23 target genomes.
[2023-03-17 04:16:06,399] [INFO] Target genome list was writen to OceanDNA-b26910/target_genomes_gtdb.txt
[2023-03-17 04:16:06,762] [INFO] Task started: fastANI
[2023-03-17 04:16:06,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgba51b707-e478-4fb5-8df5-c1523ebd3adf/OceanDNA-b26910.fa --refList OceanDNA-b26910/target_genomes_gtdb.txt --output OceanDNA-b26910/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:22,527] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:22,530] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:16:22,531] [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_013214695.1	s__R2A130 sp013214695	94.1729	171	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011087605.1	s__R2A130 sp011087605	78.463	56	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	99.98	99.97	0.98	0.98	3	-
GCA_014238155.1	s__R2A130 sp014238155	78.0176	61	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480295.1	s__R2A130 sp905480295	77.6473	54	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:22,531] [INFO] GTDB search result was written to OceanDNA-b26910/result_gtdb.tsv
[2023-03-17 04:16:22,531] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:22,532] [INFO] DFAST_QC result json was written to OceanDNA-b26910/dqc_result.json
[2023-03-17 04:16:22,532] [INFO] DFAST_QC completed!
[2023-03-17 04:16:22,532] [INFO] Total running time: 0h1m8s