I use cufflinks 2.0.2
when I run cuffdiff, it gives such error
cuffdiff -o diff_out -b hg19.fa -L s2,s3 -u merged.gtf s2.bam, s3.bam
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.1.1 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
[00:18:42] Loading reference annotation and sequence.
No fasta index found for hg19.fa. Rebuilding, please wait..
Fasta index rebuilt.
[00:21:45] Inspecting maps and determining fragment length distributions.
[00:23:03] Modeling fragment count overdispersion.
> Map Properties:
> Normalized Map Mass: 1497160.24
> Raw Map Mass: 704960.07
> Number of Multi-Reads: 137482 (with 364310 total hits)
> Fragment Length Distribution: Empirical (learned)
> Estimated Mean: 108.48
> Estimated Std Dev: 20.07
> Map Properties:
> Normalized Map Mass: 1497160.24
> Raw Map Mass: 813538.05
> Number of Multi-Reads: 167211 (with 475929 total hits)
> Fragment Length Distribution: Empirical (learned)
> Estimated Mean: 107.13
> Estimated Std Dev: 19.17
[00:23:04] Calculating preliminary abundance estimates
> Processing Locus chr7:75625836-75651212 [********************* ] 85%
WARNING: Multi-Hit not found (75684299,75687306).
> Processing Locus chr9:135822455-135826943 [*********************** ] 95%
WARNING: Multi-Hit not found (135895425,135895543).
> Processed 21567 loci. [*************************] 100%
[00:46:04] Learning bias parameters.
Bus error: 10
It stops at learning bias and shows bus error.
Anyone knows how to solve this problem.
Thank you!
when I run cuffdiff, it gives such error
cuffdiff -o diff_out -b hg19.fa -L s2,s3 -u merged.gtf s2.bam, s3.bam
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.1.1 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
[00:18:42] Loading reference annotation and sequence.
No fasta index found for hg19.fa. Rebuilding, please wait..
Fasta index rebuilt.
[00:21:45] Inspecting maps and determining fragment length distributions.
[00:23:03] Modeling fragment count overdispersion.
> Map Properties:
> Normalized Map Mass: 1497160.24
> Raw Map Mass: 704960.07
> Number of Multi-Reads: 137482 (with 364310 total hits)
> Fragment Length Distribution: Empirical (learned)
> Estimated Mean: 108.48
> Estimated Std Dev: 20.07
> Map Properties:
> Normalized Map Mass: 1497160.24
> Raw Map Mass: 813538.05
> Number of Multi-Reads: 167211 (with 475929 total hits)
> Fragment Length Distribution: Empirical (learned)
> Estimated Mean: 107.13
> Estimated Std Dev: 19.17
[00:23:04] Calculating preliminary abundance estimates
> Processing Locus chr7:75625836-75651212 [********************* ] 85%
WARNING: Multi-Hit not found (75684299,75687306).
> Processing Locus chr9:135822455-135826943 [*********************** ] 95%
WARNING: Multi-Hit not found (135895425,135895543).
> Processed 21567 loci. [*************************] 100%
[00:46:04] Learning bias parameters.
Bus error: 10
It stops at learning bias and shows bus error.
Anyone knows how to solve this problem.
Thank you!