Hi All,
I'm tophatting some data, and it's giving me a strange error:
left_kept_reads_missing.fq is, indeed, missing. Any idea what's going on here?
I'm tophatting some data, and it's giving me a strange error:
Code:
$ nohup nice tophat ../bowtie_dbs/dpse_chromosomes GSM499403_Dpseudo_R23s_8_bowtie_75.txt.fq,GSM499403_Dpseudo_R33s_5_bowtie_75.txt.fq,GSM49943_Dpseudo_R33s_6_bowtie_75.txt.fq &> tophat_io2 & $ # Time Passes $ cat tophat_io2 nohup: ignoring input [Tue May 4 15:40:52 2010] Beginning TopHat run (v1.0.13) ----------------------------------------------- [Tue May 4 15:40:52 2010] Preparing output location ./tophat_out/ [Tue May 4 15:40:53 2010] Checking for Bowtie index files [Tue May 4 15:40:53 2010] Checking for reference FASTA file [Tue May 4 15:40:53 2010] Checking for Bowtie Bowtie version: 0.12.1.0 [Tue May 4 15:40:53 2010] Checking reads seed length: 75bp format: fastq quality scale: phred33 (default) [Tue May 4 16:06:03 2010] Mapping reads against dpse_chromosomes with Bowtie [Tue May 4 18:54:28 2010] Joining segment hits Traceback (most recent call last): File "/mnt/data/sw/bin/tophat", line 1635, in <module> sys.exit(main()) File "/mnt/data/sw/bin/tophat", line 1595, in main user_supplied_juncs) File "/mnt/data/sw/bin/tophat", line 1395, in spliced_alignment segment_len) File "/mnt/data/sw/bin/tophat", line 1085, in split_reads reads_file = open(reads_filename) IOError: [Errno 2] No such file or directory: './tophat_out/tmp//left_kept_reads_missing.fq'
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