[2023-03-19 02:05:11,578] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:11,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:11,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f2b070c-4fef-4b19-88b4-7762fdc83f4a/dqc_reference
[2023-03-19 02:05:13,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:13,264] [INFO] Task started: Prodigal
[2023-03-19 02:05:13,264] [INFO] Running command: cat /var/lib/cwl/stgc5e15af9-623e-4765-8c52-c4f93bcf2c9d/OceanDNA-b24212.fa | prodigal -d OceanDNA-b24212/cds.fna -a OceanDNA-b24212/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:18,876] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:18,876] [INFO] Task started: HMMsearch
[2023-03-19 02:05:18,876] [INFO] Running command: hmmsearch --tblout OceanDNA-b24212/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f2b070c-4fef-4b19-88b4-7762fdc83f4a/dqc_reference/reference_markers.hmm OceanDNA-b24212/protein.faa > /dev/null
[2023-03-19 02:05:19,043] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:19,044] [INFO] Found 6/6 markers.
[2023-03-19 02:05:19,052] [INFO] Query marker FASTA was written to OceanDNA-b24212/markers.fasta
[2023-03-19 02:05:19,052] [INFO] Task started: Blastn
[2023-03-19 02:05:19,052] [INFO] Running command: blastn -query OceanDNA-b24212/markers.fasta -db /var/lib/cwl/stg3f2b070c-4fef-4b19-88b4-7762fdc83f4a/dqc_reference/reference_markers.fasta -out OceanDNA-b24212/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:19,602] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:19,603] [INFO] Selected 22 target genomes.
[2023-03-19 02:05:19,603] [INFO] Target genome list was writen to OceanDNA-b24212/target_genomes.txt
[2023-03-19 02:05:19,617] [INFO] Task started: fastANI
[2023-03-19 02:05:19,617] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5e15af9-623e-4765-8c52-c4f93bcf2c9d/OceanDNA-b24212.fa --refList OceanDNA-b24212/target_genomes.txt --output OceanDNA-b24212/fastani_result.tsv --threads 1
[2023-03-19 02:05:30,055] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:30,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f2b070c-4fef-4b19-88b4-7762fdc83f4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:05:30,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f2b070c-4fef-4b19-88b4-7762fdc83f4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:05:30,056] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:05:30,056] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:05:30,056] [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 02:05:30,056] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24212/tc_result.tsv
[2023-03-19 02:05:30,056] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:05:30,057] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:30,057] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f2b070c-4fef-4b19-88b4-7762fdc83f4a/dqc_reference/checkm_data
[2023-03-19 02:05:30,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:30,062] [INFO] Task started: CheckM
[2023-03-19 02:05:30,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24212/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24212/checkm_input OceanDNA-b24212/checkm_result
[2023-03-19 02:05:49,786] [INFO] Task succeeded: CheckM
[2023-03-19 02:05:49,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:05:49,789] [INFO] ===== Completeness check finished =====
[2023-03-19 02:05:49,789] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:05:49,789] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24212/markers.fasta)
[2023-03-19 02:05:49,790] [INFO] Task started: Blastn
[2023-03-19 02:05:49,790] [INFO] Running command: blastn -query OceanDNA-b24212/markers.fasta -db /var/lib/cwl/stg3f2b070c-4fef-4b19-88b4-7762fdc83f4a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24212/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:50,529] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:50,530] [INFO] Selected 17 target genomes.
[2023-03-19 02:05:50,530] [INFO] Target genome list was writen to OceanDNA-b24212/target_genomes_gtdb.txt
[2023-03-19 02:05:50,683] [INFO] Task started: fastANI
[2023-03-19 02:05:50,683] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5e15af9-623e-4765-8c52-c4f93bcf2c9d/OceanDNA-b24212.fa --refList OceanDNA-b24212/target_genomes_gtdb.txt --output OceanDNA-b24212/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:05:53,915] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:53,920] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:05:53,920] [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_002720895.1	s__GCA-002720895 sp002720895	98.1402	186	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002717245.1	s__GCA-002720895 sp002717245	81.3463	236	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.29	99.29	0.96	0.96	2	-
GCA_902607475.1	s__GCA-002720895 sp902607475	80.9885	181	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711715.1	s__GCA-002720895 sp002711715	80.7796	103	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002937775.1	s__GCA-002720895 sp002937775	80.2817	185	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.14	99.14	0.75	0.75	2	-
GCA_002937815.1	s__PTKQ01 sp002937815	77.6791	55	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__PTKQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:05:53,920] [INFO] GTDB search result was written to OceanDNA-b24212/result_gtdb.tsv
[2023-03-19 02:05:53,921] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:05:53,921] [INFO] DFAST_QC result json was written to OceanDNA-b24212/dqc_result.json
[2023-03-19 02:05:53,921] [INFO] DFAST_QC completed!
[2023-03-19 02:05:53,921] [INFO] Total running time: 0h0m42s