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alexdobin / STAR

RNA-seq aligner
MIT License
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compressed command parameter not working #831

Open priyatamapandey opened 4 years ago

priyatamapandey commented 4 years ago

Hi, I have tried the samples input from the paper "Mapping RNA-seq reads with STAR" but when I provided the compressed file and added the --readFilesCommand zcat option, it gave me no alignment. It tool me several attempt to figured that the zipped files are not working for mapping. When I unzipped my input files and ran without --readFilesCommand I can see something in progress.out and sam file. I am crosschecking whether it is actually bug and faced by others too? I have tried it with versions 2.7.3a, 2.7.2d and 2.7.2a.

Thanks, Priya

alexdobin commented 4 years ago

Hi Priya,

aah, I just responded to your previous post with this suggestion. :) If unzipping does not work, this is most likely because you are working on a non-Linux partition, which does not accept fifo files. Please try to run mkfifo tmp1 from inside your work directory to check this. To mitigate this problem, you can point --outTmpDir to a Linux partition, while still keeping you main output on the original partition. Another option is to use the process substitution: --readFilesIn <(zcat R1.gz) <(zcat R2.gz)

Cheers Alex

priyatamapandey commented 4 years ago

Thank you for the reply. I am running on the HPC. I will let you know soon.

priyatamapandey commented 4 years ago

Hi Alex, I did not quite get the first way to mitigate this problem, So I tried the second option --readFilesIn <(zcat R1.gz) <(zcat R2.gz) but this one is still not mapping anything. When I uncompressed the same file and ran, I see few gb of bam and final.log.out file with some percentage of mapped reads summary. I have few hundreds of compressed file to process. It is taking so much space when I am uncompressing it.

Thank you for your help. Priya

alexdobin commented 4 years ago

Hi Priya,

please send me the Log.out file from the run with --readFilesIn <(zcat R1.gz) <(zcat R2.gz) .

Cheers Alex

priyatamapandey commented 4 years ago

Hi Alex, I am attaching the all the three log files to you.

Thank you, Priya

test_Log.progress.out.txt test_Log.out.txt test_Log.final.out.txt

alexdobin commented 4 years ago

Hi Priya,

aah, you are using the --twopassMode Basic . This indeed does not work with the process substituion for the fastq files. You would need to try the other option - find a local Linux partition that support the fifo files, and specify it in the --outTmpDir .

Cheers Alex