hi everyone,
I'm a beginner of linux
I have a problem with running tophat.
[2013-02-26 18:47:24] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-26 18:47:24] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 0.12.9.0
[2013-02-26 18:47:24] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-26 18:47:24] 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
[2013-02-26 18:47:24] Checking for reference FASTA file
[2013-02-26 18:47:24] Generating SAM header for test_ref
format: fastq
quality scale: phred33 (default)
[2013-02-26 18:47:24] 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)
[2013-02-26 18:47:24] Mapping left_kept_reads to genome test_ref with Bowtie
[2013-02-26 18:47:24] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
[2013-02-26 18:47:24] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
[2013-02-26 18:47:24] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
[2013-02-26 18:47:24] Mapping right_kept_reads to genome test_ref with Bowtie
[2013-02-26 18:47:24] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
[2013-02-26 18:47:24] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
[2013-02-26 18:47:24] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
[2013-02-26 18:47:24] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =127
/usr/local/bin/segment_juncs: error while loading shared libraries: libboost_thread.so.1.52.0: cannot open shared object file: No such file or directory
If anybody know, please give a comment...
thanks,
I'm a beginner of linux
I have a problem with running tophat.
[2013-02-26 18:47:24] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-26 18:47:24] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 0.12.9.0
[2013-02-26 18:47:24] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-26 18:47:24] 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
[2013-02-26 18:47:24] Checking for reference FASTA file
[2013-02-26 18:47:24] Generating SAM header for test_ref
format: fastq
quality scale: phred33 (default)
[2013-02-26 18:47:24] 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)
[2013-02-26 18:47:24] Mapping left_kept_reads to genome test_ref with Bowtie
[2013-02-26 18:47:24] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
[2013-02-26 18:47:24] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
[2013-02-26 18:47:24] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
[2013-02-26 18:47:24] Mapping right_kept_reads to genome test_ref with Bowtie
[2013-02-26 18:47:24] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
[2013-02-26 18:47:24] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
[2013-02-26 18:47:24] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
[2013-02-26 18:47:24] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =127
/usr/local/bin/segment_juncs: error while loading shared libraries: libboost_thread.so.1.52.0: cannot open shared object file: No such file or directory
If anybody know, please give a comment...
thanks,
Comment