Latency during dea for large files

[yashsondhi]

Hi, while trying to run the dea portion of the script, I get this error message

Waiting at most 5 seconds for missing files. MissingOutputException in line 29 of /ufrc/kawahara/yashsondhi/rnaseq/test_analysis_ver1_2018-10-17/Workflow/snakemake_rnaseq/RASflow/workflow/dea_genome.rules: Missing files after 5 seconds: output/test_23_march/moth/genome/dea/countGroup/Night_gene_norm.tsv output/test_23_march/moth/genome/dea/countGroup/Day_gene_norm.tsv output/test_23_march/moth/genome/dea/DEA/dea_Night_Day.tsv output/test_23_march/moth/genome/dea/DEA/deg_Night_Day.tsv This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /ufrc/kawahara/yashsondhi/rnaseq/test_analysis_ver1_2018-10-17/Workflow/snakemake_rnaseq/RASflow/.snakemake/log/2020-03-26T000012.982733.snakemake.log

[zhxiaokang]

Hi, this is simply because some errors happened during executing the command and therefore the expecting output never shows up.

The way to debug it:

1. Make sure that the required input is already there, which are

   output/test_23_march/moth/genome/dea/countGroup/Night_gene_count.tsv
   output/test_23_march/moth/genome/dea/countGroup/Day_gene_count.tsv

2. Manually run the particular command: Rscript scripts/dea_genome.R And that should give you the real reason why it failed

[yashsondhi]

Hi, I did, the script ran but did not generate any output or error message.

On Thu, Mar 26, 2020 at 6:59 AM xkzhang notifications@github.com wrote:

Hi, this is simply because some errors happened during executing the command and therefore the expecting output never shows up.

The way to debug it:

1. Make sure that the required input is already there, which are

output/test_23_march/moth/genome/dea/countGroup/Night_gene_count.tsv output/test_23_march/moth/genome/dea/countGroup/Day_gene_count.tsv

1. Manually run the particular command: Rscript scripts/dea_genome.R And that should give you the real reason why it failed

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/zhxiaokang/RASflow/issues/8#issuecomment-604364021, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEAELVOPPWSUOFLEZS4P4RLRJMYSHANCNFSM4LT53YHA .

-- Yash Sondhi

PhD Student Department of Biological Sciences Florida International University,

Member, Titli trust www.titlitrust.org

Co- editor, Moths of India www.mothsofindia.org Email: yash@ifoundbutterflies.org

[yashsondhi]

Hi, Thanks I found the bug, I did not capitalise DESeq2 in the config file. Sorry for the trouble. Cheers Yash

On Fri, Mar 27, 2020 at 11:56 PM Yash Sondhi yashsondhi@gmail.com wrote:

Hi, I did, the script ran but did not generate any output or error message.

On Thu, Mar 26, 2020 at 6:59 AM xkzhang notifications@github.com wrote:

Hi, this is simply because some errors happened during executing the command and therefore the expecting output never shows up.

The way to debug it:

1. Make sure that the required input is already there, which are

output/test_23_march/moth/genome/dea/countGroup/Night_gene_count.tsv output/test_23_march/moth/genome/dea/countGroup/Day_gene_count.tsv

1. Manually run the particular command: Rscript scripts/dea_genome.R And that should give you the real reason why it failed

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/zhxiaokang/RASflow/issues/8#issuecomment-604364021, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEAELVOPPWSUOFLEZS4P4RLRJMYSHANCNFSM4LT53YHA .

-- Yash Sondhi

PhD Student Department of Biological Sciences Florida International University,

Member, Titli trust www.titlitrust.org

Co- editor, Moths of India www.mothsofindia.org Email: yash@ifoundbutterflies.org

-- Yash Sondhi

PhD Student Department of Biological Sciences Florida International University,

Member, Titli trust www.titlitrust.org

Co- editor, Moths of India www.mothsofindia.org Email: yash@ifoundbutterflies.org