Question: Fail to delete temporary folder
1
gravatar for prabin.dm
11 weeks ago by
prabin.dm160
USA/Amherst/Umass
prabin.dm160 wrote:

I am trying to map reads with rsem-calculate-expression using STAR aligner using a loop, however I am getting an error of the STARtemp folder not being deleted after the first run, hence it is stopping the next run. What wrong I am doing ?

  1. I have changed the permission in ..\test_results folder
  2. I am running on the same number of nodes as the threads requested.

this is my code

for prefix in $(ls *.fastq.gz | rev | cut -c 12-| rev | uniq)
do
rsem-calculate-expression --star \
                        --star-path /share/pkg/star/2.7.0e/bin \
                        --star-gzipped-read-file \
                        -p 4 \
                        --paired-end \
                        "${prefix}R1.fastq.gz" "${prefix}R2.fastq.gz" \
                        ../genome_indices/rsem-star/rsem-star \
                        ../test_results2/"${prefix}res"
done

This is the error part of the output

Expression Results are written!
1000000 alignment lines are loaded!
2000000 alignment lines are loaded!
3000000 alignment lines are loaded!
4000000 alignment lines are loaded!
5000000 alignment lines are loaded!
Bam output file is generated!
Time Used for EM.cpp : 0 h 02 m 50 s

rm -rf ../test_results/G20P1sc-C05-res.temp
rm: cannot remove `../test_results/G20P1sc-C05-res.temp/.nfs000000047fe2b1c700000f07': Device or resource busy
rm: cannot remove `../test_results/G20P1sc-C05-res.temp/.nfs00000004809fdb5b00000f06': Device or resource busy
rm: cannot remove `../test_results/G20P1sc-C05-res.temp/.nfs0000000480b151e000000f09': Device or resource busy
rm: cannot remove `../test_results/G20P1sc-C05-res.temp/.nfs000000048022bb5100000f08': Device or resource busy
Fail to delete the temporary folder!

"rm -rf ../test_results/G20P1sc-C05-res.temp" failed! Plase check if you provide correct parameters/options for the pipeline!
/share/pkg/star/2.7.0e/bin/STAR --genomeDir ../genome_indices/rsem-star  --outSAMunmapped Within  --outFilterType BySJout  --outSAMattributes NH HI AS NM MD  --outFilterMultimapNmax 20  --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.04  --alignIntronMin 20  --alignIntronMax 1000000  --alignMatesGapMax 1000000  --alignSJoverhangMin 8  --alignSJDBoverhangMin 1  --sjdbScore 1  --runThreadN 4  --genomeLoad NoSharedMemory  --outSAMtype BAM Unsorted  --quantMode TranscriptomeSAM  --outSAMheaderHD \@HD VN:1.4 SO:unsorted  --outFileNamePrefix ../test_results/G20P1sc-C08-res.temp/G20P1sc-C08-res  --readFilesCommand zcat  --readFilesIn G20P1sc-C08-R1.fastq.gz G20P1sc-C08-R2.fastq.gz

EXITING because of fatal ERROR: could not make temporary directory: ../test_results/G20P1sc-C08-res.temp/G20P1sc-C08-res_STARtmp/
SOLUTION: (i) please check the path and writing permissions 
 (ii) if you specified --outTmpDir, and this directory exists - please remove it before running STAR

Jun 01 13:30:25 ...... FATAL ERROR, exiting
"/share/pkg/star/2.7.0e/bin/STAR --genomeDir ../genome_indices/rsem-star  --outSAMunmapped Within  --outFilterType BySJout  --outSAMattributes NH HI AS NM MD  --outFilterMultimapNmax 20  --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.04  --alignIntronMin 20  --alignIntronMax 1000000  --alignMatesGapMax 1000000  --alignSJoverhangMin 8  --alignSJDBoverhangMin 1  --sjdbScore 1  --runThreadN 4  --genomeLoad NoSharedMemory  --outSAMtype BAM Unsorted  --quantMode TranscriptomeSAM  --outSAMheaderHD \@HD VN:1.4 SO:unsorted  --outFileNamePrefix ../test_results/G20P1sc-C08-res.temp/G20P1sc-C08-res  --readFilesCommand zcat  --readFilesIn G20P1sc-C08-R1.fastq.gz G20P1sc-C08-R2.fastq.gz" failed! Plase check if you provide correct parameters/options for the pipeline!
shell star rsem • 147 views
ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by prabin.dm160
2
gravatar for prabin.dm
11 weeks ago by
prabin.dm160
USA/Amherst/Umass
prabin.dm160 wrote:

I found out that the . nfs000000047fe2b1c700000f07 type files are the problem.

Once I directed the output to a new folder, it solved the issue :)

ADD COMMENTlink written 11 weeks ago by prabin.dm160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1179 users visited in the last hour