I am working on a small genome of Sclerotinia sclerotiorum fungi, I have downloaded reference genome fasta and gtf files from genome browser and have used the following command to generate genome indices and it was succesful.
STAR --runThreadN 8 --runMode genomeGenerate --genomeDir ./ --genomeFastaFiles GCF_000146945.2.fa --sjdbGTFfile GCF_000146945.2_ASM14694v2.ncbiRefSeq.gtf --sjdbOverhang 149 --genomeSAindexNbases 10
I have trimmed reads from trimmomatic step and I am trying to use the following command to align the reads.
STAR --runMode alignReads --runThreadN 10 --genomeDir /path/to/Refs/ --sjdbGTFfile /path/to/Refs/GCF_000146945.2_ASM14694v2.ncbiRefSeq.gtf --sjdbOverhang 149 --readFilesIn infected_1_1_paired.fq.gz infected_1_2_paired.fq.gz --outFileNamePrefix infected_1_ --outFilterMultimapNmax 1 --outBAMsortingThreadN 12 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --outSAMattributes All --outSAMstrandField intronMotif --readFilesCommand gunzip -c
Aug 10 11:31:26 ..... started STAR run
Aug 10 11:31:27 ..... loading genome
Aug 10 11:31:28 ..... started mapping
and I am stuck here and after 4 hours it abruptly ended.
The samples that I am working with are leaf samples infected with fungi and then RNA was extracted from the infected portion. so the reads are mixed with both plant and fungi. In the beginning, I tried to align the reads to the plant genome and it ran without any error and was successful. Now when I am trying to map them with fungi but facing problems.
I tested the same command on other small test sample files with the fungal reference genome, it ran successfully without any error
Are you running out of your disk/storage quota? How much memory are you using for this job?
I have enough memory to run this. When I am running the same samples with another genome of 0.5 gb, it is running successfully. but when I try to run it with this fungal genome of 40 mb, the command is struck at ... started mapping.
If STAR is working for some other genome and not for this then you need to start looking at what is different about the fungal genome. Recreate the STAR index and make sure there are no errors there. Since we can't access/see your data this may be all we can do.
Why did you delete the post, Santhi?