I'm running tophat in a remote server and I having this error message (see below the command and the error)
Can some one tell to me what could be going on?
# LSBATCH: User input
tophat -p 4 --min-intron-length 40 --max-intron-length 2000 --library-type fr-firststrand --no-novel-juncs -G /proj/seq/data/TAIR10_Ensembl/Annotation/Archives/archive-2013-03-06-09-54-25/Genes/genes.gtf -o/--output-dir tophat/Cnaa_rep1 /proj/seq/data/TAIR10_Ensembl/Sequence/Bowtie2Index/genome AGB_SPK_02-2-Cnaa-rep1_SpikeMix1_TAGCTT_L005_R1_001.fastq.gz, AGB_SPK_02-2-Cnaa-rep1_SpikeMix1_TAGCTT_L006_R1_001.fastq.gz
------------------------------------------------------------
Exited with exit code 1.
Resource usage summary:
CPU time : 0.07 sec.
Max Processes : 1
Max Threads : 1
The output (if any) follows:
Traceback (most recent call last):
File "/nas02/apps/tophat-2.0.13/bin/tophat", line 4088, in ?
sys.exit(main())
File "/nas02/apps/tophat-2.0.13/bin/tophat", line 3866, in main
prepare_output_dir()
File "/nas02/apps/tophat-2.0.13/bin/tophat", line 1242, in prepare_output_dir
os.mkdir(output_dir)
OSError: [Errno 13] Permission denied: '/--output-dir/'
Can some one tell to me what could be going on?
# LSBATCH: User input
tophat -p 4 --min-intron-length 40 --max-intron-length 2000 --library-type fr-firststrand --no-novel-juncs -G /proj/seq/data/TAIR10_Ensembl/Annotation/Archives/archive-2013-03-06-09-54-25/Genes/genes.gtf -o/--output-dir tophat/Cnaa_rep1 /proj/seq/data/TAIR10_Ensembl/Sequence/Bowtie2Index/genome AGB_SPK_02-2-Cnaa-rep1_SpikeMix1_TAGCTT_L005_R1_001.fastq.gz, AGB_SPK_02-2-Cnaa-rep1_SpikeMix1_TAGCTT_L006_R1_001.fastq.gz
------------------------------------------------------------
Exited with exit code 1.
Resource usage summary:
CPU time : 0.07 sec.
Max Processes : 1
Max Threads : 1
The output (if any) follows:
Traceback (most recent call last):
File "/nas02/apps/tophat-2.0.13/bin/tophat", line 4088, in ?
sys.exit(main())
File "/nas02/apps/tophat-2.0.13/bin/tophat", line 3866, in main
prepare_output_dir()
File "/nas02/apps/tophat-2.0.13/bin/tophat", line 1242, in prepare_output_dir
os.mkdir(output_dir)
OSError: [Errno 13] Permission denied: '/--output-dir/'
Comment