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YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
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Table 'GRCh37.chromInfo' doesn't exist // ERROR: chrom "14" not found in genome file. Exiting. #89

Open Ekomshiro opened 6 years ago

Ekomshiro commented 6 years ago

Description

Seems that Outrigger needs .chromInfo file but can't find it There is also a conflit from Ensembl vs UCSC chr naming convention

Steps to Reproduce

  1. Alignwith STAR (OK) using Ensembl GRCh37 primary assembly and gtf
  2. outrigger index with the same gtf used by STAR (OK)
  3. outrigger validate with the same .fa used by STAR

Expected behavior: This is my first run, so I'm not sure.. But based on the error message it seems that it's looking for the chromInfo file and can't find it. Then it tries to get the chromInfo file from UCSC genome browser, but since the Ensembl naming convention uses "14" instead of "chr14" it can't find it. I also tried to put the correct version of chromInfo with the .fa or my STAR output or Outrigger output, but didn't fix the problem.

Actual behavior: [What actually happened] Time Stamp Creating folder ./outrigger_output ... Time Stamp Done. Time Stamp Creating folder ./outrigger_output/index ... Time Stamp Done. Time Stamp Creating folder ./outrigger_output/index ... Time Stamp Done. Time Stamp Creating folder ./outrigger_output/index/gtf ... Time Stamp Done. Time Stamp Creating folder ./outrigger_output/junctions ... Time Stamp Done. Time Stamp Finding valid splice sites in Skipped Exon (SE) splice type ... Time Stamp Creating folder ./outrigger_output/index/se/validated ... Time Stamp Done. Time Stamp Finding valid splice sites for isoform2 of Skipped Exon events which match GT/AG or GC/AG or AT/AC... Time Stamp Finding splice sites for exon1 and exon2 ... b"ERROR 1146 (42S02) at line 1: Table 'GRCh37.chromInfo' doesn't exist\n" Commands were:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom, size from GRCh37.chromInfo" Traceback (most recent call last): File "/P/A/T/H/anaconda2/envs/outrigger-env/bin/outrigger", line 6, in sys.exit(outrigger.commandline.main()) File "/P/A/T/H/anaconda2/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 1071, in main cl = CommandLine(sys.argv[1:]) File "/P/A/T/H/anaconda2/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 344, in init self.args.func() File "/P/A/T/H/anaconda2/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 352, in validate validate.execute() File "/P/A/T/H/anaconda2/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 834, in execute exonA, exonB, splice_abbrev) File "/P/A/T/H/anaconda2/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 787, in exon_pair_splice_sites exonA, splice_abbrev, 'downstream') File "/P/A/T/H/anaconda2/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 800, in individual_exon_splice_sites exon_bed, self.genome, self.fasta, direction) File "/P/A/T/H/anaconda2/envs/outrigger-env/lib/python3.5/site-packages/outrigger/validate/check_splice_sites.py", line 57, in read_splice_sites flanked = bed.flank(l=left, r=right, s=True, genome=genome) File "/P/A/T/H/anaconda2/envs/outrigger-env/lib/python3.5/site-packages/pybedtools/bedtool.py", line 806, in decorated result = method(self, *args, **kwargs) File "/P/A/T/H/anaconda2/envs/outrigger-env/lib/python3.5/site-packages/pybedtools/bedtool.py", line 337, in wrapped decode_output=decode_output, File "/P/A/T/H/anaconda2/envs/outrigger-env/lib/python3.5/site-packages/pybedtools/helpers.py", line 356, in call_bedtools raise BEDToolsError(subprocess.list2cmdline(cmds), stderr) pybedtools.helpers.BEDToolsError: Command was:

bedtools flank -s -r 2 -l 0 -i ./outrigger_output/index/se/exon1.bed -g /tmp/pybedtools.ghiu8lqg.tmp

Error message was: ERROR: chrom "14" not found in genome file. Exiting.

Versions

Ubuntu 14.04 Anaconda 2 Outrigger version 1.1.1 installed with anaconda Outrigger calls Python 3.5.5 in virtual env created with anaconda

Ekomshiro commented 6 years ago

I found the solution..

After the --genome I put the location of my .chromInfo file and it worked.

fuhao1216 commented 3 years ago

I found the solution..

After the --genome I put the location of my .chromInfo file and it worked.

HI! What is chrominfo file ,how can i get it

liuyu988 commented 2 years ago

I found the solution..

After the --genome I put the location of my .chromInfo file and it worked.

Hi，would you give the details for getting the .chromInfo? thanks a lot!

liuyu988 commented 2 years ago

chromInfo

I suppose that after -g, wo should input a genome.chrom.sizes file.