Kallisto failure No such file abundance.tsv

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María Carolina Gallego Iradi

Dec 13, 2020, 9:17:29 AM12/13/20
to Alternative Splicing and Functional Prediction
Good afternoon:
I saw your video online at https://www.youtube.com/watch?v=Jylu-V7FmpY 
and I am trying AltAnalyze for use it with bulk RNAseq using my fastq. I followed your directions but I got an error all the time. Could you please help me to fix this issue?

This is the log

Pre-processing input files
Using AltDatabase/kallisto/0.43.1/PC/bin/kallisto.exe
Building kallisto index file...
Running kallisto on: sample1 ... kallisto failed due to an unknown error (report to altanalyze.org help).
Trying without BAM file creation.
Re-Building kallisto index file...
kallisto failed due to an unknown error (report to altanalyze.org help).
Traceback (most recent call last):
  File "RNASeq.pyc", line 5283, in runKallisto
  File "RNASeq.pyc", line 5409, in importTPMs
IOError: [Errno 2] No such file or directory: u'C:/Users/Carol/Desktop/kallisto///ExpressionInput/kallisto/sample1/abundance.tsv'

Chris G

Apr 8, 2021, 2:50:55 PM4/8/21
to Alternative Splicing and Functional Prediction

I have the same problem. has anyone a solution?




Nathan Salomonis

Apr 8, 2021, 2:59:34 PM4/8/21
to Alternative Splicing and Functional Prediction, christian...@gmail.com
Hi Chris,

The issue is likely the naming of the FASTQ files, with the software not recognizing the names properly (read1, read2, fastq.gz). For example, the software should look for extensions besides fastq or fastq.gz, (e.g., fq.gz) but doesn't in the current release, only the current source code version. If this is the case, simply renaming these files will fix this. Is this the case? Could you share one of the names?


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