Hello!
I have repeatedly experienced the same error when running tophat and despite trying to solve the problem have had no luck... The command line I use is located below:
./tophat --keep-tmp -G Homo_sapiens.GRCh37.66.gtf -p 8 -M -o /Users/jasonserviss/Desktop/Tophat\ results e66humanWP NG-6038_iPSD199_lib10333_1_sequence.fastq NG-6038_iPSD199_lib10333_2_sequence.fastq
And the error is listed here:
[2012-10-30 02:06:44] Building Bowtie index from Homo_sapiens.GRCh37.66.fa
[2012-10-30 02:37:17] Mapping left_kept_reads to transcriptome Homo_sapiens.GRCh37.66 with Bowtie
[2012-10-30 03:57:37] Mapping right_kept_reads to transcriptome Homo_sapiens.GRCh37.66 with Bowtie
[2012-10-30 05:20:01] Resuming TopHat pipeline with unmapped reads
Traceback (most recent call last):
File "./tophat", line 4035, in <module>
sys.exit(main())
File "./tophat", line 4002, in main
user_supplied_deletions)
File "./tophat", line 3423, in spliced_alignment
if not nonzeroFile(initial_reads[0]) and \
File "./tophat", line 1119, in nonzeroFile
samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 672, in __init__
errread, errwrite)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1202, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
I have looked through the forum and found 2 suggestions, one stating that the subprocess.py file is missing and that is causing the error. So I checked and it seems as though the file is present in the directory. As well, another person suggested the this error occurs when Bowtie is not in the PATH but this doesn't seem to be the case since the mapping with bowtie completes successfully and bowtie, tophat, and samtools are all in the same location on my computer...
I would be really thankful for any advice that you could offer to help me solve this issue!!
Kind Regards,
Jason
I have repeatedly experienced the same error when running tophat and despite trying to solve the problem have had no luck... The command line I use is located below:
./tophat --keep-tmp -G Homo_sapiens.GRCh37.66.gtf -p 8 -M -o /Users/jasonserviss/Desktop/Tophat\ results e66humanWP NG-6038_iPSD199_lib10333_1_sequence.fastq NG-6038_iPSD199_lib10333_2_sequence.fastq
And the error is listed here:
[2012-10-30 02:06:44] Building Bowtie index from Homo_sapiens.GRCh37.66.fa
[2012-10-30 02:37:17] Mapping left_kept_reads to transcriptome Homo_sapiens.GRCh37.66 with Bowtie
[2012-10-30 03:57:37] Mapping right_kept_reads to transcriptome Homo_sapiens.GRCh37.66 with Bowtie
[2012-10-30 05:20:01] Resuming TopHat pipeline with unmapped reads
Traceback (most recent call last):
File "./tophat", line 4035, in <module>
sys.exit(main())
File "./tophat", line 4002, in main
user_supplied_deletions)
File "./tophat", line 3423, in spliced_alignment
if not nonzeroFile(initial_reads[0]) and \
File "./tophat", line 1119, in nonzeroFile
samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 672, in __init__
errread, errwrite)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1202, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
I have looked through the forum and found 2 suggestions, one stating that the subprocess.py file is missing and that is causing the error. So I checked and it seems as though the file is present in the directory. As well, another person suggested the this error occurs when Bowtie is not in the PATH but this doesn't seem to be the case since the mapping with bowtie completes successfully and bowtie, tophat, and samtools are all in the same location on my computer...
I would be really thankful for any advice that you could offer to help me solve this issue!!
Kind Regards,
Jason
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