Hello all,
I am trying to perform alignments using TopHat2 and am receiving a gtf_to_fasta error message.
My command is the following:
$tophat -p 8 -G genes.gtf -o C1_R1_thout genome C1_R1_1.fq C1_R1_2.fq
The output:
[2014-07-28 15:40:04] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-07-28 15:40:04] Checking for Bowtie
Bowtie version: 2.2.3.0
[2014-07-28 15:40:05] Checking for Samtools
Samtools version: 0.1.19.0
[2014-07-28 15:40:05] Checking for Bowtie index files (genome)..
[2014-07-28 15:40:05] Checking for reference FASTA file
[2014-07-28 15:40:05] Generating SAM header for genome
[2014-07-28 15:40:05] Reading known junctions from GTF file
[2014-07-28 15:40:09] 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)
[2014-07-28 15:45:43] Building transcriptome data files C1_R1_thout/tmp/genes
[FAILED]
Error: gtf_to_fasta returned an error.
When I look at the output error file "g2f.err", I see the following:
dyld: lazy symbol binding failed: Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
Referenced from: /usr/local/bin/gtf_to_fasta
Expected in: /usr/lib/libstdc++.6.dylib
dyld: Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
Referenced from: /usr/local/bin/gtf_to_fasta
Expected in: /usr/lib/libstdc++.6.dylib
Has anyone had similar problems? Thanks!
James
I am trying to perform alignments using TopHat2 and am receiving a gtf_to_fasta error message.
My command is the following:
$tophat -p 8 -G genes.gtf -o C1_R1_thout genome C1_R1_1.fq C1_R1_2.fq
The output:
[2014-07-28 15:40:04] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-07-28 15:40:04] Checking for Bowtie
Bowtie version: 2.2.3.0
[2014-07-28 15:40:05] Checking for Samtools
Samtools version: 0.1.19.0
[2014-07-28 15:40:05] Checking for Bowtie index files (genome)..
[2014-07-28 15:40:05] Checking for reference FASTA file
[2014-07-28 15:40:05] Generating SAM header for genome
[2014-07-28 15:40:05] Reading known junctions from GTF file
[2014-07-28 15:40:09] 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)
[2014-07-28 15:45:43] Building transcriptome data files C1_R1_thout/tmp/genes
[FAILED]
Error: gtf_to_fasta returned an error.
When I look at the output error file "g2f.err", I see the following:
dyld: lazy symbol binding failed: Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
Referenced from: /usr/local/bin/gtf_to_fasta
Expected in: /usr/lib/libstdc++.6.dylib
dyld: Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
Referenced from: /usr/local/bin/gtf_to_fasta
Expected in: /usr/lib/libstdc++.6.dylib
Has anyone had similar problems? Thanks!
James
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