alexdobin
commented
3 years ago Hi Mat,
the best solution is to switch to a more recent STAR release, preferably the latest 2.7.8a, it will work with up to 2x300b reads. If you want to stay with 2.4.2a, you would need to recompile it after changing a line in the IncludeDefine.h file to look like this
define DEF_readSeqLengthMax 650
Cheers Alex
Hi everybody, I'm using a script which call STAR 2.4.2a in order to produce results obtained by a TARGET-seq experiment (https://github.com/albarmeira/TARGET-seq).
Usually, the script works well because library has been sequenced through an Illumina Miseq 2x150 bp sequencing. Last run has been produced by a 2x250 bp sequencing.
When I ran the script that call STAR in this way:
my $STAR_cmd = $config{STAR_EXECUTABLE}; $STAR_cmd .= ' ' . '--limitBAMsortRAM 10000000000'; if ($amplcn_count < scalar(keys %samples)) { $STAR_cmd .= ' ' . '--genomeLoad LoadAndKeep'; } else { $STAR_cmd .= ' ' . '--genomeLoad LoadAndRemove'; } $STAR_cmd .= ' ' . '--genomeDir ' . $config{STAR_INDEX_DIR}; $STAR_cmd .= ' ' . "--readFilesIn $fwd_fastq $rev_fastq"; $STAR_cmd .= ' ' . '--readFilesCommand zcat'; $STAR_cmd .= ' ' . "--outFileNamePrefix $amplcn_out_dir"; $STAR_cmd .= ' ' . '--runThreadN ' . $config{STAR_NUM_THREADS}; $STAR_cmd .= ' ' . "--outTmpDir $amplcn_tmp_dir"; $STAR_cmd .= ' ' . '--outReadsUnmapped Fastx'; $STAR_cmd .= ' ' . '--outSAMtype BAM Unsorted';
I obtained this error
EXITING because of FATAL ERROR in reads input: Lread of the pair = 501 while DEF_readSeqLengthMax=500 Read Name=@M04849:199:000000000-JF7KV:1:1101:16176:1378 SOLUTION: increase DEF_readSeqLengthMax in IncludeDefine.h and re-compile STAR
I searched for instructions to resolve this error but I did not find any tutorial.
How i can increase DEF_readSeqLengthMax in IncludeDefine.h and re-compile STAR? Are there other solutions?
Thank you very much
Mat