Stuck at the 'started mapping' step

[ERA]

Hello Alex,

 

Could you tell me why STAR is stuck at the following step?

Feb 01 10:08:47 ..... started STAR run

Feb 01 10:08:47 ..... loading genome

Feb 01 10:47:16 ..... started mapping

 

And there is this error message in the Log file

EXITING because of fatal input ERROR: could not open readFilesIn=Read1

Feb 01 10:08:30 ...... FATAL ERROR, exiting

 

My paired-end reads seemed to be fine.

-rwxr-xr-- Feb  1 00:36 read_1_trimmed.fq

-rwxr-xr-- Feb  1 00:30 read_2_trimmed.fq

 

And the code I run was:

STAR --runThreadN 24 --genomeDir refGenome_indexStar --readFilesIn read_1_trimmed.fq read_2_trimmed.fq --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --quantMode TranscriptomeSAM --outFilterType BySJout --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outSAMmapqUnique Integer0to255 –outReadsUnmapped --alignMatesGapMax 50000

 

Thanks,

ERA

[Alexander Dobin]

Hi @ERA

could you please send me the Log.out file. It seems like STAR did not recognize the --readFilesIn read_1_trimmed.fq read_2_trimmed.fq entry.

Cheers

Alex

[ERA]

Hi Alex,

This is the Log.out file.

Thanks a lot,

ERA

[Alexander Dobin]

Hi ERA,

if you look in the Log.out file at the line marked with 

##### Command Line:

you should see the command line as STAR sees it. It looks like there are some strange symbols there next to readFilesIn and outReadsUnmapped options, which STAR does not recognize as --, and so ignores these options.

Also, --outSAMmapqUnique should be an actual number 0-255, not a string.

Cheers

Alex

[Zoe Ward]

Hi Alex,

I appear to have a similar problem. I have check the Logout file and can't seem to find anything out of the ordinary (I have check the correct paths and that there is nothing wrong with the files).

I also checked the STARtmp directory and found the following:

cat readsCommand_read1

exec > "C1_STARtmp/tmp.fifo.read1"

echo FILE 0

zcat      "/media/chi/zoe/RNAseq/fastq_trimmed/C1_fwd_paired.fastq.gz"

 cat readsCommand_read2

exec > "C1_STARtmp/tmp.fifo.read2"

echo FILE 0

zcat      "/media/chi/zoe/RNAseq/fastq_trimmed/C1_rev_paired.fastq.gz"

cat readFilesIn.info

-rwxr-xr-x 1 root HCSgroup 504078865 Feb  8 12:55 /media/chi/zoe/RNAseq/fastq_trimmed/C1_rev_paired.fastq.gz

It looks as though it's only reading in the reverse read??? Do you agree? I can't seem to find anything wrong with the #### command in the Logout file (which I have attached)??

Any advice is much appreciated.

Zoe.

[Alexander Dobin]

Hi Zoe,

please try to unzip the files (or small portions of them, say 1M reads for read1/2) and run STAR without the --readFilesCommand zcat option.

Log.out file does not have anything suspicious. Is there any error message, or STAR just hangs? What does top show?

Cheers

Alex

[Zoe Ward]

Hi Alex,

That seemed to work thank you!

Many thanks.