Entering edit mode
7.5 years ago
murphy.charlesj
▴
100
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:
- STAR 2-pass
- Added read group information with Picard
- Marked (but did not remove) duplicates with Picard
- SplitNCigarReads with GATK
- Realigned around indels with GATK
- 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.
