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splicebox / PsiCLASS

Simultaneous multi-sample transcript assembler for RNA-seq data
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PsiCLASS running into an error #8

Open sagnikbanerjee15 opened 4 years ago

sagnikbanerjee15 commented 4 years ago

Hello,

I am using PsiCLASS to generate assemblies from over 100 samples. I keep getting this error:

head: write error: Broken pipe head: write error

It is producing all the gtf files though. Please help.

Thank you.

mourisl commented 4 years ago

Can you run "samtools view your_first_bam_file | head -1000"?

You can run psiclass with option "--mateIdx 0" to avoid this operation. If you did not receive the message "Found mate read id index suffix(.1 or /1)", your previous running should be fine.

sagnikbanerjee15 commented 4 years ago

Thank you for your reply.

I am facing a different kind of issue now. I have launched the execution with --mateIdx 0. I have waited more than 6 hours but the run does not produce any results and does not even finish. It produces empty gtf files. I was monitoring the log files and after a while, nothing was being written to it but the program kept running. There are a total of 122 bam files.

Thank you.

mourisl commented 4 years ago

Can you run "samtools view your_first_bam_file | head -1000"? Because PsiCLASS internally uses this pipe to determine whether read id has ".1" or "/1" suffix. It should not throw out an error, so I guess there is something wrong with the bam file or system.

Can you also show me what has been printed on the screen after running?

Thanks.

sagnikbanerjee15 commented 4 years ago

Hello,

Here is the snapshot of the samtools view command. I am using STAR to map the reads which

Thank you.

image

sagnikbanerjee15 commented 4 years ago

Hello,

Were you able to find the reason behind the error?

Thank you.

mourisl commented 4 years ago

I guessing there is a fairly complicated gene structure and PsiCLASS might be stuck there. Did you use the option --bamGroup? Thanks.

sagnikbanerjee15 commented 4 years ago

Hello,

I tried running PsiCLASS both with and without the --bamGroup option. For both cases, the execution got stuck. Is there any way to determine abnormalities from the bam file?

Thank you.

mourisl commented 4 years ago

I just made an update to handle complicated genes more efficiently. Could you please also share the log file "{psiclass_}classes.log" with me? Thanks.

sagnikbanerjee15 commented 4 years ago

Hello,

I tried running the latest version but I am still running into problems. The execution gets stuck after a certain point of time. The log file is huge. Please access it from https://drive.google.com/open?id=1TU3HsbyavEIt9pPuXGrTwzLjQTiTGfHW.

Thank you.

mourisl commented 3 years ago

Hello,

I just made a update to PsiCLASS, which should be the ultimate solution to the "stuck" issue. Could you please give it a try on the samples PsiCLASS failed to finish?

Thanks