Cuffdiff - Error in running cuffdiff by using the merged transcriptome assembly along with the BAM files from TopHat

Question

[evashan96]

hello everyone, I ran cuffdiff using following command:

cuffdiff -o ./diff_out -b ./genome.fa -p 7 -L c1,c2 -u ./merged.gtf \
./accepted_hits_S1.bam,./accepted_hits_S2.bam,./accepted_hits_S3.bam ./accepted_hits_S4.bam,./accepted_hits_S5.bam,./accepted_hits_S6.bam,./accepted_hits_S7.bam,./accepted_hits_S8.bam,./accepted_hits_S9.bam,./accepted_hits_S10.bam,./accepted_hits_11.bam,./accepted_hits_S12.bam

And the output was:

Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
[16:26:46] Loading reference annotation and sequence.
Warning: couldn't find fasta record for 'CHR_MG117_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_MG153_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.
Warning: couldn't find fasta record for 'CHR_MG3231_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG3561_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG3562_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG3609_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_MG3833_PATCH'!
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_MG4151_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_MG4209_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_MG4212_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_MG4214_PATCH'!
This contig will not be bias corrected.
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_MG4248_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4249_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4254_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4255_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4261_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4264_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4265_PATCH'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'CHR_MG4266_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 'GL456210.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GL456211.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GL456212.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GL456216.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GL456219.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GL456221.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GL456233.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GL456239.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GL456350.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GL456354.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GL456372.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GL456381.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'GL456385.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'JH584292.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'JH584293.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'JH584294.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'JH584295.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'JH584296.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'JH584297.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'JH584298.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'JH584299.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'JH584303.1'!
This contig will not be bias corrected.
Warning: couldn't find fasta record for 'JH584304.1'!
This contig will not be bias corrected.
Killed

please help me out.

[ATpoint]

Please highlight code and data examples as well as error messages:

[evashan96]

cuffdiff -o ./diff_out -b ./genome.fa -p 7 -L c1,c2 -u ./merged.gtf \ ./accepted_hits_S1.bam,./accepted_hits_S2.bam,./accepted_hits_S3.bam ./accepted_hits_S4.bam,./accepted_hits_S5.bam,./accepted_hits_S6.bam,./accepted_hits_S7.bam,./accepted_hits_S8.bam,./accepted_hits_S9.bam,./accepted_hits_S10.bam,./accepted_hits_11.bam,./accepted_hits_S12.bam

this is the code.

there is no error, i just want to know why the process killed itself. The last line of the ouput states killed. why is that?

[ATpoint]

Please highlight code and data examples as well as error messages:

with the code option in the format bar, the one with the red box in my comment above :)

[evashan96]

cuffdiff -o ./diff_out -b ./genome.fa -p 7 -L c1,c2 -u ./merged.gtf \ ./accepted_hits_S1.bam,./accepted_hits_S2.bam,./accepted_hits_S3.bam ./accepted_hits_S4.bam,./accepted_hits_S5.bam,./accepted_hits_S6.bam,./accepted_hits_S7.bam,./accepted_hits_S8.bam,./accepted_hits_S9.bam,./accepted_hits_S10.bam,./accepted_hits_11.bam,./accepted_hits_S12.bam

Answer 1

[Benn]

Check this previous post and the answer of Devon Ryan.