I have designed this script to run Bowtie2 on paired end fastq data files for a spliceoform investigation. However, it fails as it can't find the -1 input file, this is very strange as the name is correct...
Please help as i'm not sure what to try?
tophat -o 9-0GS_bowtie2_for_splicegrapher -j TAIR10_GFF3_genes.gff --no-convert-bam -a 10 -g 1 -F 0 -p 6 --segment-length=28 --segment-mismatches=0 -i 40 -I 5000 --min-coverage-intron=40 --max-coverage-intron=5000 --min-segment-intron=40 --max-segment-intron=5000 TAIR10_chr_all.bt2 -1 9-0GS_AGTCAA_run298_trimmed_1.fastq -2 9-0GS_AGTCAA_run298_trimmed_2.fastq
[2012-08-09 15:17:04] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-08-09 15:17:04] Checking for Bowtie
Bowtie version: 2.0.0.7
[2012-08-09 15:17:04] Checking for Samtools
Samtools version: 0.1.18.0
[2012-08-09 15:17:04] Checking for Bowtie index files
[2012-08-09 15:17:04] Checking for reference FASTA file
Warning: Could not find FASTA file TAIR10_chr_all.bt2.fa
[2012-08-09 15:17:04] Reconstituting reference FASTA file from Bowtie index
Executing: /usr/local/bin/bowtie2-inspect TAIR10_chr_all.bt2 > 9-0GS_bowtie2_for_splicegrapher/tmp/TAIR10_chr_all.bt2.fa
[2012-08-09 15:17:09] Generating SAM header for TAIR10_chr_all.bt2
Traceback (most recent call last):
File "/usr/local/bin/tophat", line 3948, in <module>
sys.exit(main())
File "/usr/local/bin/tophat", line 3808, in main
params.read_params = check_reads_format(params, reads_list)
File "/usr/local/bin/tophat", line 1725, in check_reads_format
zf = ZReader(f_name, params)
File "/usr/local/bin/tophat", line 1678, in __init__
self.file=open(filename)
IOError: [Errno 2] No such file or directory: '-1'
But the directory is there, with the correct name, i've also tried with the whole root directory and got the same message.
Any ideas?
Please help as i'm not sure what to try?
tophat -o 9-0GS_bowtie2_for_splicegrapher -j TAIR10_GFF3_genes.gff --no-convert-bam -a 10 -g 1 -F 0 -p 6 --segment-length=28 --segment-mismatches=0 -i 40 -I 5000 --min-coverage-intron=40 --max-coverage-intron=5000 --min-segment-intron=40 --max-segment-intron=5000 TAIR10_chr_all.bt2 -1 9-0GS_AGTCAA_run298_trimmed_1.fastq -2 9-0GS_AGTCAA_run298_trimmed_2.fastq
[2012-08-09 15:17:04] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-08-09 15:17:04] Checking for Bowtie
Bowtie version: 2.0.0.7
[2012-08-09 15:17:04] Checking for Samtools
Samtools version: 0.1.18.0
[2012-08-09 15:17:04] Checking for Bowtie index files
[2012-08-09 15:17:04] Checking for reference FASTA file
Warning: Could not find FASTA file TAIR10_chr_all.bt2.fa
[2012-08-09 15:17:04] Reconstituting reference FASTA file from Bowtie index
Executing: /usr/local/bin/bowtie2-inspect TAIR10_chr_all.bt2 > 9-0GS_bowtie2_for_splicegrapher/tmp/TAIR10_chr_all.bt2.fa
[2012-08-09 15:17:09] Generating SAM header for TAIR10_chr_all.bt2
Traceback (most recent call last):
File "/usr/local/bin/tophat", line 3948, in <module>
sys.exit(main())
File "/usr/local/bin/tophat", line 3808, in main
params.read_params = check_reads_format(params, reads_list)
File "/usr/local/bin/tophat", line 1725, in check_reads_format
zf = ZReader(f_name, params)
File "/usr/local/bin/tophat", line 1678, in __init__
self.file=open(filename)
IOError: [Errno 2] No such file or directory: '-1'
But the directory is there, with the correct name, i've also tried with the whole root directory and got the same message.
Any ideas?
Comment