Error parsing Bowtie output file

[SoberDog]

Hi, I'm running the SpliceSeq locally to process my own RNA-seq data. But I get an error "Error parsing Bowtie output file" My SpliceSeq version is 2.1, the bowtie version is 0.12.9, the java version is 1.8.0_271 and my OS is win10 20H2.

I have checked the set up against the website instructions, but I can't seem to fix this.

The ebwt files have already been created by bowtie-build.exe.

The log file is just like this: log_file.txt

Kind Regards,

Owen

[mryaninsilico]

So first recommendation would be to use the newer SpliceSeq - 2.3 at http://projects.insilico.us.com/SpliceSeq_2.3/SpliceSeq.zip

It looks like a parsing issue with the bowtie output. Could you look in the processing directory for the bowtie alignment results. The line that it is complaining about (because it does not have a tab character) is: SRR11557592.8045 D90VQ5P1:154:H. Is there any chance you could search for that line in the bowtie output and get a few lines before and after that line and post it?

[SoberDog]

Hi, Mike

The last three lines of bowtie output are as follows.

SRR11557592.8052 D90VQ5P1:154:H27WWBCXX:1:1101:6588:22924 length=75 - 3315|40104:26-146;(41899)40105:0-6;(41901)40106:0-116; 166 TGTGCATTACATTTGGAAAAAAATGTGAATCAGTCACTACTGGAACTGCACAAACTGGCCACTGACAAAAATGAC EIHIHIHF<1C1CDEG<HHHG?IHFD<<1CGCEHG<EHHHGEHIHIHIHG1FHD1HECFHF1HGIIIIIIDDDDD 4

SRR11557592.8052 D90VQ5P1:154:H27WWBCXX:1:1101:6588:22924 length=75 + 3314|40099:18-1411; 871 GTCATTTTTGTCAGTGGCCAGTTTGTGCAGTTCCAGTAGTGACTGATTCACATTTTTTTCCAAATGTAATGCACA DDDDDIIIIIIGH1FHFCEH1DHF1GHIHIHIHEGHHHE<GHECGC1<<DFHI?GHHH<GEDC1C1<FHIHIHIE 4

SRR11557592.8045 D90VQ5P1:154:H

I tried to turn up the logging level and get a new log file. NewLogFile.txt

Thanks,

Owen

[mryaninsilico]

Owen,

Looks like bowtie died mid-processing. Maybe the computer shut down or went to sleep? Because the file is there, SpliceSeq thinks it has completed and will try to process the output each time you start it. Best bet would be to delete or move the bowtie results file so SpliceSeq will run the alignment again.

If you have the logging level in log4j.xml turned up , it should print out the command line used to run bowtie. If it fails again, I would suggest running bowtie manually using the command line from the logs. It may print something to the screen to indicate why it is failing.

Mike

From: SoberDog [mailto:notifications@github.com] Sent: Wednesday, December 09, 2020 7:49 PM To: MD-Anderson-Bioinformatics/SpliceSeq Cc: Michael Ryan; Comment Subject: Re: [MD-Anderson-Bioinformatics/SpliceSeq] Error parsing Bowtie output file (#8)

Hi, Mike

The last three lines of bowtie output are as follows.

SRR11557592.8052 D90VQ5P1:154:H27WWBCXX:1:1101:6588:22924 length=75 - 3315|40104:26-146;(41899)40105:0-6;(41901)40106:0-116; 166 TGTGCATTACATTTGGAAAAAAATGTGAATCAGTCACTACTGGAACTGCACAAACTGGCCACTGACAAAAATGAC EIHIHIHF<1C1CDEG<HHHG?IHFD<<1CGCEHG<EHHHGEHIHIHIHG1FHD1HECFHF1HGIIIIIIDDDDD 4

SRR11557592.8052 D90VQ5P1:154:H27WWBCXX:1:1101:6588:22924 length=75 + 3314|40099:18-1411; 871 GTCATTTTTGTCAGTGGCCAGTTTGTGCAGTTCCAGTAGTGACTGATTCACATTTTTTTCCAAATGTAATGCACA DDDDDIIIIIIGH1FHFCEH1DHF1GHIHIHIHEGHHHE<GHECGC1<<DFHI?GHHH<GEDC1C1<FHIHIHIE 4

SRR11557592.8045 D90VQ5P1:154:H

I tried to turn up the logging level and get a new log file. NewLogFile.txt https://github.com/MD-Anderson-Bioinformatics/SpliceSeq/files/5669544/NewLogFile.txt

Thanks,

Owen

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