Cufflinks segmentation fault

Question

[murphy.charlesj]

I' am running cufflinks on some RNA-seq:

cufflinks -o . -b Mus_musculus.GRCm38.dna.primary_assembly.fa -G Mus_musculus.GRCm38.79.gtf test.40m.bam

I get the following error:

You are using Cufflinks v2.2.1, which is the most recent release.
[15:58:59] Loading reference annotation and sequence.
Warning: couldn't find fasta record for 'CHR_MG4222_MG3908_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4237_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4209_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4151_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MMCHR1_CHORI29_IDD5_1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4136_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4213_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG3829_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4180_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG3833_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG153_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4211_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG132_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4212_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4214_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG184_PATCH'!
This contig will not be bias corrected.
[16:00:09] Inspecting reads and determining fragment length distribution.
> Processing Locus 6:85431988-85446435         [****                     ]  18%Segmentation fault

I don't think this is a memory issue since I tried running the command on a machine with 1.5TB of memory. Moreover, I' am running cufflinks after the following steps:

1. STAR 2-pass
2. Added read group information with Picard
3. Marked (but did not remove) duplicates with Picard
4. SplitNCigarReads with GATK
5. Realigned around indels with GATK
6. Performed base recalibration with GATK

However, I do not get this issue if I run Cufflinks on the BAM file before steps 2-6. I've run my pipeline on close to 200 samples, but I seem to get this error only on four of them.

Answer 1

[murphy.charlesj]

The solution is here in another post I made.