noddevil4949
commented
6 days ago Hi,
Thanks for your question. It looks like 1_DRRcontigs.fasta did not generate properly. Maybe have a check of the input fasta file "DRRcontigs.fasta" to see if it is intact and not compressed? Please provide a bit more details of the fasta file (e.g., the size of the file, head lines, etc.) if this error persists.
Cheers, BASALT team
Dear BASALT Team: Thanks for such an amazing tool. However I am running the 'Building Bowtie2 index' of BASALT with two problems.
Command: BASALT -a DRRcontigs.fasta -s filtered1.fastq,filtered2.fastq -t 32 -m 384 --min-cpn 50 --max-ctn 10
First, During Building Bowtie2 index: Settings: Output files: "1_DRRcontigs.fasta..bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void:8, int:4, long:8, size_t:8 Input files DNA, FASTA: 1_DRRcontigs.fasta Warning: Empty fasta file: '1_DRRcontigs.fasta' Warning: All fasta inputs were empty Total time for call to driver() for forward index: 00:00:00 Error: Encountered internal Bowtie 2 exception (#1) Command: /work/home/acsxe0ht0t/miniconda3/envs/NEWBASALT/bin/bowtie2-build-s --wrapper basic-0 1_DRRcontigs.fasta 1_DRRcontigs.fasta Done!
Second, During Mapping datasets to contigs/scaffolds: (ERR): "1_DRRcontigs.fasta" does not exist or is not a Bowtie 2 index Exiting now ... [E::hts_open_format] Failed to open file 1_DNA-1.sam samtools view: failed to open "1_DNA-1.sam" for reading: No such file or directory Cannot open the infile 1_DNA-1.sam mv: cannot stat ‘condensed.cytoscape.connections.tab’: No such file or directory rm: cannot remove ‘1_DNA-1.sam’: No such file or directory
Any response would be greatly appreciated!