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qqwang-berkeley / JUM

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
MIT License
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Perl Error due to a sample not having AS on one contig #44

Closed rLannes closed 1 year ago

rLannes commented 1 year ago

Hi!

I encounter the following Error Running JUM_A: ERROR: Database file output_long_intron_sorted.gff contains chromosome X_3, but the query file does not. Please rerun with the -g option for a genome file. See documentation for details.

the following command shows results for all except one sample. grep X_3 control_vs_Treat/*Aligned.out.sorted.bed

I believe the error come from the process_sortedbam() function During the intersection steps!

May be a way to resolve this issue is to extract from all sample the @SQ tag and merge them to build a bed genome.txt file. and then give this genome to the bedtools intersect inside process_sortedbam.

Could you help me? my perl is very bad....

qqwang-berkeley commented 1 year ago

This is really weird. If the samples are processed properly you should not see this error. Did you make sure that the process_sortedbam() function ran successfully on every sample? Sometimes due to the memory limit certain sample processing steps were terminated in the backstage without notifying you. If you want, I can share with you a modified version of JUM that perform sample processing sequentially but not in parallel so that you can be sure every sample is pre-processed properly.

rLannes commented 1 year ago

Hi, thank you for your answer. That was the error, I increased the memory available and the error disappeared. I should have closed the issue, sorry for that