Tophat [Errno 8] Exec format error

[Gaurav_genomics]

I have installed everything and all the necessary libraries required but its giving the error:

[Errno 8] Exec format error

The full output with the test data is as follows:

tophat -r 20 test_ref reads_1.fq reads_2.fq

[2013-03-13 09:57:12] Beginning TopHat run (v2.0.8)
-----------------------------------------------
[2013-03-13 09:57:12] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-03-13 09:57:12] Checking for Samtools
Samtools version: 0.1.18.0
[2013-03-13 09:57:12] Checking for Bowtie index files
Warning: we do not recommend to have both Bowtie1 and Bowtie2 indexes in the same directory
the genome sequence (*.fa) may not be compatible with one of them
[2013-03-13 09:57:12] Checking for reference FASTA file
[2013-03-13 09:57:12] Generating SAM header for test_ref
format: fastq
quality scale: phred33 (default)
[2013-03-13 09:57:13] Preparing reads
left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
[2013-03-13 09:57:13] Mapping left_kept_reads to genome test_ref with Bowtie2
[2013-03-13 09:57:13] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie2 (1/3)
[2013-03-13 09:57:13] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie2 (2/3)
[2013-03-13 09:57:13] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie2 (3/3)
[2013-03-13 09:57:13] Mapping right_kept_reads to genome test_ref with Bowtie2
[2013-03-13 09:57:13] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie2 (1/3)
[2013-03-13 09:57:14] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie2 (2/3)
[2013-03-13 09:57:14] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie2 (3/3)
[2013-03-13 09:57:14] Searching for junctions via segment mapping
[Errno 8] Exec format error


Kindly help.

[ercfrtz]

I am getting the same error but at an earlier step. More information on what is happening would be great.

[2013-06-20 08:33:39] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2013-06-20 08:33:39] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-06-20 08:33:39] Checking for Samtools
Samtools version: 0.1.18.0
[2013-06-20 08:33:39] Checking for Bowtie index files
[2013-06-20 08:33:39] Checking for reference FASTA file
[2013-06-20 08:33:39] Generating SAM header for ../nagrp2/ercfrtz/bos_taurus_tophat_sort
format: fastq
quality scale: phred33 (default)
[2013-06-20 08:34:02] Preparing reads
[FAILED]
[Errno 8] Exec format error

[GenoMax]

[Errno 8] Exec format error seems to refer to an OS error.

What OS are you running tophat on?

Have you looked at the tophat log directory to see if there is any additional information in the logs.