gzip: stdout: Bad file descriptor gzip issue

[Jack Yen]

Hi,

I couldn't figure out what's wrong with the STAR command I use to pass fastq.gz zipped file to my linux box. I keep getting error messages

"gzip: stdout: Bad file descriptor" 

I tried both "zcat" and "gunzip -c" options but getting same error and empty BAM. (                          Number of input reads |       0" ) 

--readFilesCommand gunzip -c \

--readFilesCommand zcat  \

Could someone help me or point me in the right direction? Thanks

command I used:

STAR --runThreadN 20 \

--genomeDir /home/lee/reference/hg19/starindex \

--outFileNamePrefix MiniR1_S3_ \

--outSAMattrRGline ID:1 "SM:MiniR1_S3" \

--outSAMattributes NH NM MD \

--outSAMtype BAM SortedByCoordinate \

--limitBAMsortRAM 12000000000 \

--outSAMunmapped Within \

--outSAMmapqUnique 50 \

--readFilesIn /media/fs02/TMB/170926_NB501920_0028_AHC5WMBGX3/CS156185_S1/CS156185_S1_R1_001.fastq.gz /media/fs02/TMB/170926_NB501920_0028_AHC5WMBGX3/CS156185_S1/CS156185_S1_R2_001.fastq.gz \

--readFilesCommand gunzip -c \

--sjdbGTFfile "/media/fs02/reference/hg19/annotation/genes.gtf" \

--outFilterType BySJout \

--outSJfilterCountUniqueMin -1 2 2 2 \

--outSJfilterCountTotalMin -1 2 2 2 \

--outFilterIntronMotifs RemoveNoncanonical \

--twopassMode Basic

[Alexander Dobin]

Hi Jack,

I think you have figure that this is the problem with the partition (FAT?) not capable of working with fifo files.

You have a few options:

1. Supply a path to a partition (any standard Linux) that supports fifo files with --outTmpDir /path/to/temp/dir/

2. Use the process substitution: --readFilesIn <(zcat read1.gz) <(zcat read2.gz), and no --readFilesCommand

3. Unzip the files before mapping.

Cheers

Alex

[Hemant]

 zcat (option 2) doesn't work. 

[Alexander Dobin]

Hi Hemant,

please send me your command line and the Log.out file.

Cheers

Alex