refrence genome

[adi8897]

Hi im not sure if i built the reference genome ok the slrum files told me its done [IR_finder_venv] <46|0>adi8897@moriah-gw-01:~/adi8897/IR_finder_venv/IRFinder-1.3.0/REF/Human-GRCh38-release110% cat slurm-22221567.out Launching reference build process. The full build might take hours. <Phase 1: STAR Reference Preparation> STAR --runMode genomeGenerate --genomeDir /sci/home/adi8897/adi8897/IR_finder_venv/IRFinder-1.3.0/REF/Human-GRCh38-release110/STAR --genomeFastaFiles /sci/home/adi8897/adi8897/IR_finder_venv/IRFinder-1.3.0/REF/Human-GRCh38-release110/genome.fa --sjdbGTFfile /sci/home/adi8897/adi8897/IR_finder_venv/IRFinder-1.3.0/REF/Human-GRCh38-release110/transcripts.gtf --sjdbOverhang 150 --runThreadN 128 &>> log-star-build-ref.log STAR version: 2.7.10a compiled: 2022-04-11T09:13:40+03:00 :/usr/local/hurcs/STAR/STAR-2.7.10a/source Apr 19 07:42:33 ..... started STAR run Apr 19 07:42:33 ... starting to generate Genome files Apr 19 07:43:12 ..... processing annotations GTF Apr 19 07:43:34 ... starting to sort Suffix Array. This may take a long time... Apr 19 07:43:50 ... sorting Suffix Array chunks and saving them to disk... Apr 19 07:52:56 ... loading chunks from disk, packing SA... Apr 19 07:55:09 ... finished generating suffix array Apr 19 07:55:09 ... generating Suffix Array index Apr 19 07:58:17 ... completed Suffix Array index Apr 19 07:58:17 ..... inserting junctions into the genome indices Apr 19 08:01:16 ... writing Genome to disk ... Apr 19 08:01:20 ... writing Suffix Array to disk ... Apr 19 08:01:55 ... writing SAindex to disk Apr 19 08:02:02 ..... finished successfully <Phase 2: Mapability Calculation> Apr 19 08:02:02 ... mapping genome fragments back to genome... Apr 19 08:12:20 ... sorting aligned genome fragments... [bam_sort_core] merging from 0 files and 128 in-memory blocks... Apr 19 08:14:52 ... indexing aligned genome fragments... Apr 19 08:15:14 ... filtering aligned genome fragments by chromosome/scaffold... Apr 19 08:16:44 ... merging filtered genome fragments... Apr 19 08:17:28 ... calculating regions for exclusion... Apr 19 08:22:28 ... cleaning temporary files... <Phase 3: IRFinder Reference Preparation> Apr 19 08:22:31 ... building Ref 1... Apr 19 08:23:02 ... building Ref 2... Apr 19 08:23:04 ... building Ref 3... Apr 19 08:23:04 ... building Ref 4... Apr 19 08:23:25 ... building Ref 5... Apr 19 08:23:49 ... building Ref 6... Apr 19 08:23:50 ... building Ref 7... Apr 19 08:23:52 ... building Ref 8... Apr 19 08:23:53 ... building Ref 9... Apr 19 08:23:53 ... building Ref 10b... Apr 19 08:23:53 ... building Ref 11b... Apr 19 08:23:53 ... building Ref 12b... [IR_finder_venv] <47|0>adi8897@moriah-gw-01:~/adi8897/IR_finder_venv/IRFinder-1.3.0/REF/Human-GRCh38-release110% but i don't see finish q this is the command i ran ~/adi8897/IR_finder_venv/IRFinder-1.3.0/bin/IRFinder -m BuildRefProcess -r ~/adi8897/IR_finder_venv/IRFinder-1.3.0/REF/Human-GRCh38-release110 -e ~/adi8897/IR_finder_venv/IRFinder-1.3.0/REF/extra-input-files/RNA.SpikeIn.ERCC.fasta.gz -R ~/adi8897/IR_finder_venv/IRFinder-1.3.0/REF/extra-input-files/Human_hg38_nonPolyA_ROI.bed

I'm thinking there is a problem but i don't know what

[dg520]

@adi8897 Hi, is there also a slurm-22221567.err file that captures the standard error? If so, what is the content? I need more specific information about this issue to provide insights.

[adi8897]

there is no output files but it did not wrote finished successfully. i don't understand if this is the way it should be ended <Phase 3: IRFinder Reference Preparation> Apr 19 08:22:31 ... building Ref 1... Apr 19 08:23:02 ... building Ref 2... Apr 19 08:23:04 ... building Ref 3... Apr 19 08:23:04 ... building Ref 4... Apr 19 08:23:25 ... building Ref 5... Apr 19 08:23:49 ... building Ref 6... Apr 19 08:23:50 ... building Ref 7... Apr 19 08:23:52 ... building Ref 8... Apr 19 08:23:53 ... building Ref 9... Apr 19 08:23:53 ... building Ref 10b... Apr 19 08:23:53 ... building Ref 11b... Apr 19 08:23:53 ... building Ref 12b...

this is how step3 should be end? is there step 4?

the folder Mapability contain only this file MapabilityExclusion.bed.gz.

I'm wondering because after that my analysis did not ran well and i think it because of the reference genome

[dg520]

@adi8897 Check your IRFinder folder next to Mapability. If every file there, other than intergenic.ROI.bed, is non-empty, your reference is built successfully. There is no line explicitly saying building success. It will only print a line to indicate failure when things go wrong.

What do you mean "analysis did not ran well"? Do you refer to your previous post that you haven't seen differential IR? If so, I don't think it is reference's problem. I replied to you in that post as well. You can follow up there.

[adi8897]

ok thank you i will check everything. tanks for the fast response!