I am having a trouble while running tophat2.
I am using tophat2 (v2.0.11), Bowtie2 (v2.2.2) and samtools (v0.1.19).
The command line that I am using is as follows:
$ tophat -G /path/to/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf --transcriptome-index /path/to/transcriptome_data/known -o /path/to/out -p 8 /path/to/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome /path/to/read_1.fastq.gz /path/to/read_2.fastq.gz
The last few lines of the error message is:
[2014-04-18 01:59:45] Resuming TopHat pipeline with unmapped reads
Traceback (most recent call last):
File "./tophat", line 4084, in <module>
sys.exit(main())
File "./tophat", line 4050, in main
user_supplied_deletions)
File "./tophat", line 3452, in spliced_alignment
if not nonzeroFile(initial_reads[0]) and \
File "./tophat", line 1159, in nonzeroFile
samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Can anyone of you help me to solve the problem.
Thank you.
I am using tophat2 (v2.0.11), Bowtie2 (v2.2.2) and samtools (v0.1.19).
The command line that I am using is as follows:
$ tophat -G /path/to/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf --transcriptome-index /path/to/transcriptome_data/known -o /path/to/out -p 8 /path/to/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome /path/to/read_1.fastq.gz /path/to/read_2.fastq.gz
The last few lines of the error message is:
[2014-04-18 01:59:45] Resuming TopHat pipeline with unmapped reads
Traceback (most recent call last):
File "./tophat", line 4084, in <module>
sys.exit(main())
File "./tophat", line 4050, in main
user_supplied_deletions)
File "./tophat", line 3452, in spliced_alignment
if not nonzeroFile(initial_reads[0]) and \
File "./tophat", line 1159, in nonzeroFile
samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Can anyone of you help me to solve the problem.
Thank you.
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