genomeGenerate error, plenty of free space on disk

[A R]

Hello there,
I am trying to use STAR on the rainbow trout genome. I have the same issue as mentioned here, but limiting RAM does not solve it.
In short, the genomeGenerate function returns a "lack of disk space" error, as follows. However, it seems there is plenty of empty space (per the last line). Computer details follow the code:

=============
sudo STAR --runMode genomeGenerate --genomeChrBinNbits 16 --genomeSAindexNbases 12 --limitSjdbInsertNsj 469030 --genomeSAsparseD 2 --runThreadN 10 --genomeDir /media/snarc1/8TB_Seagate/trout_2_data/ArleeGenome/ --readFilesCommand zcat --genomeFastaFiles /media/snarc1/8TB_Seagate/trout_2_data/ArleeGenome/OmykA_1.1/GCF_013265735.2_USDA_OmykA_1.1_genomic.fna --sjdbGTFfile /media/snarc1/8TB_Seagate/trout_2_data/ArleeGenome/OmykA_1.1/GCF_013265735.2_USDA_OmykA_1.1_genomic.gtf --limitGenomeGenerateRAM 20000000000
Jan 22 18:51:02 ..... started STAR run
Jan 22 18:51:02 ... starting to generate Genome files
Jan 22 18:51:36 ..... processing annotations GTF
Jan 22 18:51:57 ... starting to sort Suffix Array. This may take a long time...
Jan 22 18:52:05 ... sorting Suffix Array chunks and saving them to disk...
Jan 22 19:05:52 ... loading chunks from disk, packing SA...
Jan 22 19:06:29 ... finished generating suffix array
Jan 22 19:06:29 ... generating Suffix Array index
Jan 22 19:06:57 ... completed Suffix Array index
Jan 22 19:06:59 ..... inserting junctions into the genome indices
Jan 22 19:10:23 ... writing Genome to disk ...
Jan 22 19:10:41 ... writing Suffix Array to disk ...

Genome_genomeGenerate.cpp:390:genomeGenerate: exiting because of *OUTPUT FILE* error: could not write the output file /media/snarc1/8TB_Seagate/trout_2_data/ArleeGenome//SA
fail()=1 ; bad()=1
Error while trying to write chunk # 4; 8589934588 bytes
File size full = 10407851107 bytes
File size on disk = 4294967295 bytes
Solution: check that you have enough space on the disk
Empty space on disk = 951396728832 bytes

Jan 22 19:10:46 ...... FATAL ERROR, exiting

=============

Details:
I am running STAR 2.7.7a on Ubuntu 18.04.5 LTS
Memory: 93.1 GiB
Processor: Intel® Xeon(R) Gold 5120 CPU @ 2.20GHz × 56
GNOME: 3.28.2
Disk: 250.0 GB

The files are stored on an 8 TB external hard drive with 958.8 GB free.

I do have root privileges but I cannot change the ulimit.

Here is the output of ulimit -a command:
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 381039
max locked memory       (kbytes, -l) 65536
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 381039
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

Attached is the output of free -g command and the Log.out file.

Thank you in advance for your help!

Anna R.

[Alexander Dobin]

Hi Anna,

this error means that there was a problem with writing the file to the disk. Space does not seem to be a problem, so I would recommend checking the disk for errors.

Then please try to run it again. If the error persists, you may need to use a different disk. If you have ~100GB free on your 250GB main disk, you can try using it.

Cheers

Alex

[A R]

I finally figured out the error -- embarrassingly simple. I was trying to write my output files to an external hard drive, but the external hard drive does not allow files > 4GB to be written.

When I switched the genome output folder to the computer's main tower, the process finished in under 20 minutes.

Thank you!

Anna

[Alexander Dobin]

Hi Anna,

you are right, there are all kinds of trouble with non-Linux partitions. In the mapping step, you may have a problem with gzipped files, if this partition does not support the fifio files.

Cheers

Alex

[A R]

Thank you very much for the help!