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rkweku / miRador

Plant miRNA identification tool that utilizes a variety of filters to validate predicted miRNAs
GNU General Public License v3.0
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bowtie error #15

Open SamCT opened 3 months ago

SamCT commented 3 months ago

Hello,

Thank you for the tool, I am excited to put it to use. I successfully ran the test and it completed. On real data however, I get an error. My sRNA data was originally in fastq, so I converted it to .fa via seqtk since that is what was expected...

2024-06-03 10:10:06,082 - miRador - miRador - Running einverted sequentially
2024-06-03 10:20:22,703 - genome - combineIRTempFiles - Combined files 'invertedRepeats/ChromosomeAssembly_March29_Inverted_Aligns.inv and invertedRepeats/ChromosomeAssembly_March29_Inverted_Seqs.fa'
Deleting temp files
2024-06-03 10:20:22,915 - miRador - miRador - Beginning to process /folder/fa_strip/lane1-s006-indexRPI18-GTCCGC-B3_S6_R1_001_fp.fa, library 1 of 7.
2024-06-03 10:20:57,515 - library - readFasta - Time to read library /folder/fa_strip/lane1-s006-indexRPI18-GTCCGC-B3_S6_R1_001_fp.fa: 28.42 seconds
2024-06-03 10:20:57,667 - miRador - miRador - Running bowtie on /folder/fa_strip/lane1-s006-indexRPI18-GTCCGC-B3_S6_R1_001_fp.fa
2024-06-03 10:20:59,887 - library - mapper - Mapping small RNAs to the genome files for /folder/fa_strip/lane1-s006-indexRPI18-GTCCGC-B3_S6_R1_001_fp.fa
2024-06-03 10:21:04,793 - library - mapper - Something went wrong when running bowtie. Command was
bowtie genome/bowtieIndex/ChromosomeAssembly_March29 -f miRadorTempFolder/fastaLibs/lane1-s006-indexRPI18-GTCCGC-B3_S6_R1_001_fp.fa.fa -a -m 50 --best --strata -v 0 -S miRadorTempFolder/bowtieOutput/lane1-s006-indexRPI18-GTCCGC-B3_S6_R1_001_fp.fa.map -p 1 --sam-nohead --no-unal

Do you have any suggestions as to why this failed?

Thank you, Sam

rkweku commented 2 months ago

Hi Sam,

Apologies for my delayed response. Have you tried running that same bowtie command from the terminal to see what the output is from bowtie? You will likely get a much more detailed error report that way which would help in the debugging,.