STAR aligner STAR: bgzf.c:158: bgzf_open: Assertion `compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE' failed.

Question

[tedwinkent]

Hey y'all, I am quite new to RNA-seq, and I am trying to align a FASTQ file with the following command and could not get it to work :(. I have been stuck figuring out what to do for a week or so, so any help would be great! P.s. I'm running this in a high performance cluster

module load star/2.7.10b
STAR --runThreadN 50 \
--genomeDir ./ref \
--readFilesIn ${fqdir}/${fq}_1_val_1_val_1_val_1.fq.gz ${fqdir}/${fq}_2_val_2_val_2_val_2.fq.gz \
--readFilesCommand gunzip -c \
--limitGenomeGenerateRAM 70000000000 \
--sjdbGTFfile ./stringtie_oogenesis_assembled_vM25_ERCC_merge_rm_TE-mono-exon_new_rmERCC-chrY.gtf \
--outFileNamePrefix ${fq}_STAR_mm10_rmERCCchrY \
--outSAMtype BAM SortedByCoordinate \
--twopassMode Basic \
--outFilterType BySJout \
--outFilterMultimapNmax 1 \
--winAnchorMultimapNmax 50 \
--alignSJoverhangMin 8 \
--alignSJDBoverhangMin 1 \
--outFilterMismatchNmax 999 \
--outFilterMismatchNoverReadLmax 0.04 \
--alignIntronMin 20 \
--alignIntronMax 1000000 \
--alignMatesGapMax 1000000

[GenoMax]

Can you validate your fastq files? You could use validateFiles (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/validateFiles ). After downloading the util (Linux version linked, macOS available) you can add execute permissions (chmod u+x validateFiles). Finally run

validateFiles -type=fastq file1.gz file2.gz