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Error encountered when running the example #1

Closed juliefrwang closed 1 year ago

juliefrwang commented 1 year ago

Hi,

I was running the example of NOMAD v2.0.0 and followed the steps using precompiled binaries, but I received following error messages. Starting stage 1 Current time: 2023-04-10 15:43:33 Error running command: /usr/bin/time -v ../kmc -t8 -b -ci1 -cs65535 -k54 -m12 SRX14565338_SRR18431620_1.fastq.gz nomad-tmp-ec10df89b76a4283822ceeb949e63cdd/SRX14565338_SRR18431620_1 nomad-tmp-ec10df89b76a4283822ceeb949e63cdd/kmc_tmp_SRX14565338_SRR18431620_1 For details check logs/stage_1_thread-0000.log Error running command: /usr/bin/time -v ../kmc -t8 -b -ci1 -cs65535 -k54 -m12 SRX14565346_SRR18431612_1.fastq.gz nomad-tmp-ec10df89b76a4283822ceeb949e63cdd/SRX14565346_SRR18431612_1 nomad-tmp-ec10df89b76a4283822ceeb949e63cdd/kmc_tmp_SRX14565346_SRR18431612_1 For details check logs/stage_1_thread-0002.log Error running command: /usr/bin/time -v ../kmc -t8 -b -ci1 -cs65535 -k54 -m12 SRX14565342_SRR18431616_1.fastq.gz nomad-tmp-ec10df89b76a4283822ceeb949e63cdd/SRX14565342_SRR18431616_1 nomad-tmp-ec10df89b76a4283822ceeb949e63cdd/kmc_tmp_SRX14565342_SRR18431616_1 For details check logs/stage_1_thread-0001.log Error running command: /usr/bin/time -v ../kmc -t8 -b -ci1 -cs65535 -k54 -m12 SRX14565361_SRR18431597_1.fastq.gz nomad-tmp-ec10df89b76a4283822ceeb949e63cdd/SRX14565361_SRR18431597_1 nomad-tmp-ec10df89b76a4283822ceeb949e63cdd/kmc_tmp_SRX14565361_SRR18431597_1 For details check logs/stage_1_thread-0003.log Exiting because of previous error

The .log file detailed the error: Cannot open temporary file nomad-tmp-ec10df89b76a4283822ceeb949e63cdd/kmc_tmp_SRX14565342_SRR18431616_1/kmc_00253.bin.

I'd love to know what's the issue. Thank you!

marekkokot commented 1 year ago

Hi, KMC keeps hundreds of files open. Usually, this is not an issue, and the number of opened files may be changed with ulimit -n <value>. If you cannot run this command in most cases it is OK to run KMC in RAM-only mode (it does not use intermediate files in such a case). This may be enabled by running nomad with --kmc_use_RAM_only_mode. If, however, you are dealing with large input files (I mean when a single sample is large) you may have some RAM issues. In such a case it may be worth contacting your administrator to increase the limit of opened files. If this is not possible we may expose a parameter allowing to set the number of intermediate files. Let me know if that helps.