Can not run the assembly on a system with 128GB RAM

[aidashah]

I have a whole genome sequencing dataset of an insect with a genome size around 500Mb. I have tried to assemble it via Abyss but, it is killed, most probably due to RAM insufficiency. I have asked the developers and they recommended using another mode of the program. Actually, apparently, the program has two modes, one is hash table and another one is Bloom filter. The first one uses so much RAM capacity (around 200GB for a genome size of 500Mb) while the other one needs much less RAM. I have run the bloom filter mode according to ( https://github.com/bcgsc/abyss#assembling-using-a-bloom-filter-de-bruijn-graph) and it is alright for now (It is not finished yet). I am sharing this here, in case that others might encounter the same trouble in the future.

[sjackman]

Glad to hear that you got it working, and thanks for reporting your experience.

[aidashah]

Dear Shuan, My run has been finished withe following messages: Minimum and maximum distance are set to -63 and 971 bp. error: no @SQ records in the SAM header make: [tpittrim10643-3.dist] Error 1 make: Deleting file `tpittrim10643-3.dist' As, it is my first experience, I don't know whether it is finished successfully or not.

[sjackman]

The run was unsuccessful. Please report the exact command that you ran and the complete log file of your run.

[aidashah]

The following command I have run: abyss-pe name=tpittrim10643 k=64 in='trimmed10-R1.fastq trimmed10-R2.fastq' B=64G H=3 kc=3 v=-v After the following commands the assembly has been stopped.

FR Stats mean: 398.1 median: 392 sd: 93.62 n: 147696758 min: 58 max: 971 ignored: 19183 ▁▁▂▃▄▅▆▇██████▇▆▆▅▄▃▃▂▂▁▁____ sort: write failed: /tmp/sortlvR4ke: No space left on device Mate orientation FR: 147711567 (100%) RF: 4374 (0.00296%) The library tpittrim10643-3.hist is oriented forward-reverse (FR). Stats mean: 398.1 median: 392 sd: 93.62 n: 147696758 min: 58 max: 971 ▁▁▂▃▄▅▆▇██████▇▆▆▅▄▃▃▂▂▁▁____ Minimum and maximum distance are set to -63 and 971 bp. error: no @SQ records in the SAM header make: [tpittrim10643-3.dist] Error 1 make: Deleting file `tpittrim10643-3.dist'

[aidashah]

No log file is generated.

[aidashah]

Hello, I have written the command under the same issue in the github. I would be so thankful if you can take a look. Regards,

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[kmnip]

This is the relevant part of your log:

sort: write failed: /tmp/sortlvR4ke: No space left on device

Your temp directory is full. You may want to redirect the TMPDIR environment variable to your current working directory before running ABySS.

[benvvalk]

thanks @sjackman and @kmnip

[sjackman]

On some systems /var/tmp has more space than /tmp.

df -h /tmp /var/tmp
export TMPDIR=/var/tmp