search

alexdobin / STAR

RNA-seq aligner
MIT License
1.87k stars 506 forks source link

STAR read files not found #1042

Open mtcarilli opened 4 years ago

mtcarilli commented 4 years ago

Hi,

I'm attempting to align paired-end RNAseq data, which I previously trimmed using trimgalore, with STAR. STAR, however, is not finding the fastq files.

Here is my batch script:

R1=/projects/maca9088/CypA/trimmed_data/UVI_R1_val_1.fq.gz R2=/projects/maca9088/CypA/trimmed_data/UVI_R2_val_2.fq.gz

STAR --genomeDir /projects/maca9088/genomedirectory --runThreadN 8 --readFilesCommand zcat\ --readFilesIn $R1 $R2 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ./UVI samtools index ./UVIAligned.sortedByCoord.out.bam

This is the error I get: gzip: Read1.gz: No such file or directory

Which is strange because Read1.gz is not even in my command?

Thanks so much for your helo!

pabloivan commented 4 years ago

Check to see whether there is an extra space or uncommon character between the end of zcat and the beginning of --readFilesIn statement. Just type the command directly to the terminal to test for this, as sometimes when we copy/paste some malformatted chars can be passed to the command.

alexdobin commented 4 years ago

Hi @mtcarilli

Good suggestions from Pablo. It also helps to check the Log.ouit file to see if the command line was processed correctly.

Cheers Alex