transcript assembling problem by cufflinks

Question

[kuhelikadas1995]

After alignment by hisat2 tool and generation of SAM ,BAM and sorted BAM files, I gave this command for transcripts assembling:

cufflinks -o SRR1131119.sam -G Homo_sapiens.GRCh38.97.gff3 --library-type fr-firststrand --no-update-check --upper-quartile-norm  SRR1131119_sorted.bam

Then this happened.. again and again. What to do? Please help!

[00:23:01] Loading reference annotation.
[00:23:14] Inspecting reads and determining fragment length distribution.
Processed 32972 loci.                        [*************************] 100%
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges.  It is recommended that correct parameters (--frag-len-mean and --frag-len-std-dev) be provided.
Map Properties:
Normalized Map Mass: 4040892.47
Raw Map Mass: 4040892.47
Fragment Length Distribution: Truncated Gaussian (default)
   Default Mean: 200
   Default Std Dev: 80
Segmentation fault (core dumped)

[grant.hovhannisyan]

not an answer, but I'd recommend to switch to stringtie from cufflinks.

[kuhelikadas1995]

what difference would it make?? moreover during hisat2 alignmnt i used the command "--dta-cufflinks" which does the job specifically for cufflinks..

[grant.hovhannisyan]

its is newer, faster, better maintained, and can save a lot of time and nerves in a long run.

[Kristoffer Vitting-Seerup]

The main function of the -dta-cufflinks in Hisat is to ensure only longer anchors are reported. You can enable that manually with --downstream-transcriptome-assembly. Which version of Cufflinks are you running?

[kuhelikadas1995]

i am using cufflinks version 2.2.1

[Kristoffer Vitting-Seerup]

Try post an issue on the Cufflinks github instead.