tophat IOError

[seq_me_out]

I get the following error when I run Tophat, when I tested the installation of Tophat and Bowtie I didn't have any issues, any idea what's causing this?

$ tophat -r 210 -G Homo_sapiens.GRCh37.61_fix.gtf /z_program_downloads/bowtie2-2.1.0/indexes/hg19 s_1_1_sub_sequence.fq.txt, s_2_1_sub_sequence.fq.txt s_1_2_sub_sequence.fq.txt, s_2_2_sub_sequence.fq.txt

[2013-04-07 18:28:14] Beginning TopHat run (v2.0.8)
-----------------------------------------------
[2013-04-07 18:28:14] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-04-07 18:28:14] Checking for Samtools
Samtools version: 0.1.19.0
[2013-04-07 18:28:14] Checking for Bowtie index files
[2013-04-07 18:28:14] Checking for reference FASTA file
Warning: Could not find FASTA file
/z_program_downloads/bowtie2-2.1.0/indexes/hg19.fa
[2013-04-07 18:28:14] Reconstituting reference FASTA file from Bowtie index
Executing: /usr/local/bin/bowtie2-inspect
/z_program_downloads/bowtie2-2.1.0/indexes/hg19 > ./tophat_out/tmp/hg19.fa
[2013-04-07 18:30:27] Generating SAM header for /z_program_downloads/bowtie2-2.1.0/indexes/hg19
Traceback (most recent call last):
File "/usr/local/bin/tophat", line 4030, in <module>
sys.exit(main())
File "/usr/local/bin/tophat", line 3885, in main
params.read_params = check_reads_format(params, reads_list)
File "/usr/local/bin/tophat", line 1822, in check_reads_format
zf = ZReader(f_name, params)
File "/usr/local/bin/tophat", line 1775, in __init__
self.file=open(filename)
IOError: [Errno 2] No such file or directory: ''

[mastal]

tophat IOError

Hi,

you have a space after the comma in the list of the files with the first reads of the pairs.

s_1_1_sub_sequence.fq.txt, s_2_1_sub_sequence.fq.txt

try removing the space and see if that helps.

[Corn]

He, I got the same error yesterday also with PE100 data....

tophat2 -p 7 -o '/media/Data/RNAseq_DATA/SMART/rawdata/Sample_cornelis_2/tophat_try' '/media/Data/hg19/Homo_sapiens/UCSC/hg19/Sequence/BOWTIE2_INDEXES/genome' R1_trimmed.fastq R2_trimmed.fastq


[2013-04-09 10:32:59] Beginning TopHat run (v2.0.8)
-----------------------------------------------
[2013-04-09 10:32:59] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-04-09 10:32:59] Checking for Samtools
Samtools version: 0.1.18.0
[2013-04-09 10:32:59] Checking for Bowtie index files
[2013-04-09 10:32:59] Checking for reference FASTA file
[2013-04-09 10:32:59] Generating SAM header for /media/Data/hg19/Homo_sapiens/UCSC/hg19/Sequence/BOWTIE2_INDEXES/genome
format: fastq
quality scale: phred33 (default)
[2013-04-09 10:33:00] Preparing reads
left reads: min. length=20, max. length=101, 184920288 kept reads (223128 discarded)
right reads: min. length=20, max. length=101, 185066394 kept reads (77022 discarded)
[2013-04-09 12:59:35] Mapping left_kept_reads to genome genome with Bowtie2
[2013-04-09 20:05:26] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/4)
[2013-04-09 20:31:20] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/4)
[2013-04-09 20:59:56] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/4)
[2013-04-09 21:35:21] Mapping left_kept_reads_seg4 to genome genome with Bowtie2 (4/4)
[2013-04-09 22:01:33] Mapping right_kept_reads to genome genome with Bowtie2
[bam_header_read] EOF marker is absent. The input is probably truncated.
Traceback (most recent call last):
File "/usr/local/bin/tophat", line 4030, in <module>
sys.exit(main())
File "/usr/local/bin/tophat", line 3997, in main
user_supplied_deletions)
File "/usr/local/bin/tophat", line 3520, in spliced_alignment
segment_len)
File "/usr/local/bin/tophat", line 2952, in split_reads
open_output_files(prefix, num_segments, tmp_num_segments, out_segfiles, extension, params)
File "/usr/local/bin/tophat", line 2837, in open_output_files
out_segf.append(ZWriter(segfname,params.system_params))
File "/usr/local/bin/tophat", line 1788, in __init__
self.ftarget=open(filename, "wb")

[rob123king]

I'm getting a similar error, any help with this would be appreciated, see below command line output:

[2013-04-12 12:08:11] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-04-12 12:08:11] Checking for Samtools
Samtools version: 0.1.19.0
[2013-04-12 12:08:11] Checking for Bowtie index files
[2013-04-12 12:08:11] Checking for reference FASTA file
[2013-04-12 12:08:11] Generating SAM header for genome
format: fastq
quality scale: phred33 (default)
[2013-04-12 12:08:11] Reading known junctions from GTF file
[2013-04-12 12:08:13] Preparing reads
left reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
[2013-04-12 12:10:50] Creating transcriptome data files..
[2013-04-12 12:10:54] Building Bowtie index from genes.fa
[2013-04-12 12:15:43] Mapping left_kept_reads to transcriptome genes with Bowtie2
[2013-04-12 12:20:40] Mapping right_kept_reads to transcriptome genes with Bowtie2
[2013-04-12 12:25:57] Resuming TopHat pipeline with unmapped reads
Traceback (most recent call last):
File "/home/robking/Downloads/tophat/tophat", line 4030, in <module>
sys.exit(main())
File "/home/robking/Downloads/tophat/tophat", line 3997, in main
user_supplied_deletions)
File "/home/robking/Downloads/tophat/tophat", line 3430, in spliced_alignment
if not nonzeroFile(initial_reads[0]) and \
File "/home/robking/Downloads/tophat/tophat", line 1149, in nonzeroFile
samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
File "/usr/lib/python2.7/subprocess.py", line 679, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1249, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

[rob123king]

Tried to re-download tophat and make it myself rather than the premade version and don't have boost installed so installing this now and may be the problem for this error at least for me.

[seq_me_out]

My issue was the spaces, I made tophat with the most recent version of boost and it works great.