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.
[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.
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