[2023-03-15 23:42:29,663] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:42:29,663] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:42:29,663] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5d75499-3732-4496-938d-168870d03ec5/dqc_reference
[2023-03-15 23:42:31,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:42:31,275] [INFO] Task started: Prodigal
[2023-03-15 23:42:31,275] [INFO] Running command: cat /var/lib/cwl/stg724444f3-0929-4033-aefd-7c4148b015b7/OceanDNA-b40631.fa | prodigal -d OceanDNA-b40631/cds.fna -a OceanDNA-b40631/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:42:38,448] [INFO] Task succeeded: Prodigal
[2023-03-15 23:42:38,449] [INFO] Task started: HMMsearch
[2023-03-15 23:42:38,449] [INFO] Running command: hmmsearch --tblout OceanDNA-b40631/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5d75499-3732-4496-938d-168870d03ec5/dqc_reference/reference_markers.hmm OceanDNA-b40631/protein.faa > /dev/null
[2023-03-15 23:42:38,632] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:42:38,632] [INFO] Found 6/6 markers.
[2023-03-15 23:42:38,646] [INFO] Query marker FASTA was written to OceanDNA-b40631/markers.fasta
[2023-03-15 23:42:38,646] [INFO] Task started: Blastn
[2023-03-15 23:42:38,647] [INFO] Running command: blastn -query OceanDNA-b40631/markers.fasta -db /var/lib/cwl/stgb5d75499-3732-4496-938d-168870d03ec5/dqc_reference/reference_markers.fasta -out OceanDNA-b40631/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:42:39,217] [INFO] Task succeeded: Blastn
[2023-03-15 23:42:39,218] [INFO] Selected 30 target genomes.
[2023-03-15 23:42:39,218] [INFO] Target genome list was writen to OceanDNA-b40631/target_genomes.txt
[2023-03-15 23:42:39,236] [INFO] Task started: fastANI
[2023-03-15 23:42:39,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg724444f3-0929-4033-aefd-7c4148b015b7/OceanDNA-b40631.fa --refList OceanDNA-b40631/target_genomes.txt --output OceanDNA-b40631/fastani_result.tsv --threads 1
[2023-03-15 23:42:54,654] [INFO] Task succeeded: fastANI
[2023-03-15 23:42:54,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5d75499-3732-4496-938d-168870d03ec5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:42:54,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5d75499-3732-4496-938d-168870d03ec5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:42:54,655] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:42:54,655] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:42:54,655] [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 23:42:54,655] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40631/tc_result.tsv
[2023-03-15 23:42:54,655] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:42:54,655] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:42:54,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5d75499-3732-4496-938d-168870d03ec5/dqc_reference/checkm_data
[2023-03-15 23:42:54,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:42:54,661] [INFO] Task started: CheckM
[2023-03-15 23:42:54,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40631/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40631/checkm_input OceanDNA-b40631/checkm_result
[2023-03-15 23:43:17,877] [INFO] Task succeeded: CheckM
[2023-03-15 23:43:17,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:43:17,880] [INFO] ===== Completeness check finished =====
[2023-03-15 23:43:17,880] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:43:17,880] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40631/markers.fasta)
[2023-03-15 23:43:17,882] [INFO] Task started: Blastn
[2023-03-15 23:43:17,882] [INFO] Running command: blastn -query OceanDNA-b40631/markers.fasta -db /var/lib/cwl/stgb5d75499-3732-4496-938d-168870d03ec5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40631/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:43:19,034] [INFO] Task succeeded: Blastn
[2023-03-15 23:43:19,036] [INFO] Selected 16 target genomes.
[2023-03-15 23:43:19,036] [INFO] Target genome list was writen to OceanDNA-b40631/target_genomes_gtdb.txt
[2023-03-15 23:43:19,048] [INFO] Task started: fastANI
[2023-03-15 23:43:19,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg724444f3-0929-4033-aefd-7c4148b015b7/OceanDNA-b40631.fa --refList OceanDNA-b40631/target_genomes_gtdb.txt --output OceanDNA-b40631/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:43:27,537] [INFO] Task succeeded: fastANI
[2023-03-15 23:43:27,540] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:43:27,540] [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_002401885.1	s__UBA9145 sp002401885	83.389	313	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016762975.1	s__UBA9145 sp016762975	80.9468	258	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016762995.1	s__UBA9145 sp016762995	80.7337	271	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	96.79	96.79	0.78	0.78	2	-
GCA_905478195.1	s__UBA9145 sp003483155	77.2868	122	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.23	98.96	0.87	0.81	6	-
--------------------------------------------------------------------------------
[2023-03-15 23:43:27,541] [INFO] GTDB search result was written to OceanDNA-b40631/result_gtdb.tsv
[2023-03-15 23:43:27,541] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:43:27,542] [INFO] DFAST_QC result json was written to OceanDNA-b40631/dqc_result.json
[2023-03-15 23:43:27,542] [INFO] DFAST_QC completed!
[2023-03-15 23:43:27,542] [INFO] Total running time: 0h0m58s