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alexdobin / STAR

RNA-seq aligner
MIT License
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Error: STAR quality string length is not equal to sequence length #1786

Open PratitiA opened 1 year ago

PratitiA commented 1 year ago

Hello,

I am using STAR 2.7.10b

my genome generate command is -

STAR --runMode genomeGenerate --genomeDir /athena/wenlab/scratch/pra4003/LIP_ESCs/esc-2il-p15/genome_index --genomeFastaFiles Mus_musculus.GRCm39.dna_sm.primary_assembly.fa --sjdbGTFfile Mus_musculus.GRCm39.109.gtf --runThreadN 12

I used following command for alignReads:

STAR --runMode alignReads --genomeDir /athena/wenlab/scratch/pra4003/LIP_ESCs/esc-2il-p15/genome_index --outSAMtype BAM SortedByCoordinate --readFilesIn /athena/wenlab/scratch/pra4003/LIP_ESCs/esc-2il-p15/trimmed_R1_combined_fastq --runThreadN 10

and got the following error:

Mar 09 15:54:26 ..... started STAR run Mar 09 15:54:26 ..... loading genome Mar 09 15:54:47 ..... started mapping

EXITING because of FATAL ERROR in reads input: short read sequence line: 0 Read Name=@A00814:150:HKLGTDRXX:1:1228:17906:34538 Read Sequence==== DEF_readNameLengthMax=50000 DEF_readSeqLengthMax=650

Mar 09 15:55:14 ...... FATAL ERROR, exiting

I install STAR on my Ubuntu server with Miniconda and anaconda.

I don't know why I am seeing this error, I have all the files I require for alignReads.

your help and assistance would be greatly appreciated.

Best, Pratiti

alexdobin commented 1 year ago

Hi Pratiti,

this indicates a problem with the FASTQ file, it looks like the sequence for a read is missing, probably after trimming. When trimming, you need to make sure that the trimmer does not output empty sequence. Instead, output one or more N.