Tophat Error: It Tries To Execute Lines In Fastq Files
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8.2 years ago
newDNASeqer ▴ 730

From a previous RNASeq data that was analyzed a year ago, I tried to use the unmapped data and align it to a different species genome (mouse), and I used PiCard to convert the unmapped.bam file (generated by Tophat) to fastq format. Then I tried to run the following tophat command, but got the following error message:

> tophat -p 4 \
--bowtie1 \
-z 0 \
--library-type fr-unstranded \
--GTF illumina_mouse_37_1.gtf \
--segment-mismatches 2 \
--segment-length 25 \
-o tophat_OUT \
illumina_mouse_37_1 \
fastq/file1.fastq.gz

-------------------------------------------------------------------------------
> [2013-07-30 13:06:28] Checking for Bowtie
Bowtie version:     0.12.7.0
[2013-07-30 13:06:28] Checking for Samtools
Samtools version:     0.1.18.0
[2013-07-30 13:06:28] Checking for Bowtie index files
[2013-07-30 13:06:28] Checking for reference FASTA file
[2013-07-30 13:06:28] Generating SAM header for /usr/local/bowtie_indicies/mouse_ncbi_37_2
Traceback (most recent call last):
File "/usr/local/bin/tophat-2.0.6/tophat", line 4022, in <module>
sys.exit(main())
File "/usr/local/bin/tophat-2.0.6/tophat", line 3877, in main
File "/usr/local/bin/tophat-2.0.6/tophat", line 1814, in check_reads_format
File "/usr/local/bin/tophat-2.0.6/tophat", line 1767, in __init__
self.file=open(filename)
IOError: [Errno 2] No such file or directory: ' '
./fastq/file1.fastq.gz: line 8: syntax error near unexpected token newline'
./fastq/file1.fastq.gz: line 8: BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIFFFIIIIIFIFFFFFFFFFFFFFFFFFBFBB<<'


why does tophat complain that those lines in fastq file are not commands? why does Tophat execute those lines in FastQ files? I don't understand, please help. thank you

tophat bowtie error • 3.2k views
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can you please verify the command line and errors. It appears that the error comes from a different command. Your indices as specified are illumina_mouse_37_1 but the actual path in the error is usr/local/bowtie_indicies/mouse_ncbi_37_2

this suggests to me that the error results from a different command. The error would be the one reported if you tried to execute the fastq file directly, perhaps you have it marked as executable and you have a semicolon in the real command line