Hi!
I'm trying to convert my .fastq files to .sam doing the alignment and continue pre-processing in order to obtain the read counts, but i've reiteratively received an error processing a .fastq of 4'27 GB and 107073636 lines.
the code is:
./bwa mem /path/to/Homo_sapiens.GRCh38.dna.primary_assembly.fa /path/to/.fastq > /path/to/.sam
and the error is:
[fputs] File too large
Thanks!
what is your filesystem? fat32 ? you cannot write a file with size > 4 G : https://en.wikipedia.org/wiki/File_Allocation_Table#FAT32
The maximum possible size for a file on a FAT32 volume is 4 GiB minus 1 byte or 4,294,967,295 (232 − 1) bytes.
Hi Pierre, thank you for answering!
That was exactly the problem... I'll try with APFS
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You can avoid the intermediate sam file to save space and write directly to bam:
bwa mem genome.fa reads.fastq | samtools sort -o alignment.bamperfect, thank you!!