• Find some reads
• Find a test genome
• Look for Kofler's original exercises

Related to RG tags

I got the following error while running the example dataset. The file 2R.mpileup.log is empty - possibly a problem with fifo. System administrator checked and mkfifo is definitely installedon the system being used. The version installed is 8.28.
System administrator also tried recreating the software (running the snakemake pipeline) on another of our development machines and hit other problems with packages that are definitely installed but it doesn’t seem to like it.
I'm currently testing the popoolation2 part by running each step separately from command line.

Activating conda environment: /home/dyern/lstm_scratch/smsk_popoolation/.snakemake/conda/5af75ca214322542d38ca9626894a8ef

mkfifo: cannot create fifo 'results/mpileup/filt/pop2/pop2.2R.mpileup': Operation not permitted

[Mon Dec 6 12:29:00 2021]

Error in rule mpileup_popoolation_filter_indels:

jobid: 27

output: results/mpileup/filt/pop2/pop2.2R.mpileup, results/mpileup/filt/pop2/pop2.2R.mpileup.gz

log: results/mpileup/filt/pop2/pop2.2R.mpileup.log (check log file(s) for error message)

conda-env: /home/dyern/lstm_scratch/smsk_popoolation/.snakemake/conda/5af75ca214322542d38ca9626894a8ef

shell:

   

    mkfifo results/mpileup/filt/pop2/pop2.2R.mpileup



    (cat results/mpileup/filt/pop2/pop2.2R.mpileup | gzip --fast > results/mpileup/filt/pop2/pop2.2R.mpileup.gz &)



    perl src/popoolation_1.2.2/basic-pipeline/filter-pileup-by-gtf.pl             --input <(gzip --decompress --stdout results/mpileup/raw/pop2/pop2.2R.mpileup.gz)             --gtf results/mpileup/filt/pop2/pop2.2R.gtf             --output results/mpileup/filt/pop2/pop2.2R.mpileup         2> results/mpileup/filt/pop2/pop2.2R.mpileup.log 1>&2

   

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Mon Dec 6 12:29:03 2021]

Finished job 6.

33 of 71 steps (46%) done

Shutting down, this might take some time.

Exiting because a job execution failed. Look above for error message

Complete log: /home/dyern/lstm_scratch/smsk_popoolation/.snakemake/log/2021-12-06T122740.426984.snakemake.log

picard uses by default just 1Gb of RAM. It causes problems when working on big files.

Add something in config.yaml to expand it and modify the map and mpileup steps

When sorting, samtools writes a bunch of temporary files next to the final bam. if snakemake is interrupted, it removes some of the files, but not the intermediate ones. Use /tmp/ to store the intermediate files and for easier cleanup later.

Hi, thank you for your contributions!
While I want to install smsk_popoolation after installing anaconda3, I met an issue like the following.
git clone https://github.com/jlanga/smsk_popoolation.git smsk_popoolation #run well
cd smsk_popoolation # run well
snakemake --use-conda --create-envs-only #dont't work and get the message

The program 'snakemake' is currently not installed. To run 'snakemake' please ask your administrator to install the package 'snakemake'.

so I need install 'snakemake' before using snakemake or 'snakemaker' is a script of 'smsk_popoolation'?

Any reply will be welcomed.

GATK in mind (indel realigner + base recalibrator)

Working through the example data, I ran using "snakemake --use-conda --cores 24"
However, I got an error in rule "raw_extract_genome" that the 2R.fa.gz file (supplied example data) is not in gzip format. Is it the example data or the command at fault?

This may be due to an update in snakemake commands. When I tried to paste the command from the instructions "snakemake --use-conda --create-envs-only" I got the error message "snakemake: error: unrecognized arguments: --create-envs-only"
First I tried replacing with snakemake --use-conda --conda-create-envs-only but I got the following error message asking me to enter the number of cores (Error: you need to specify the maximum number of CPU cores to be used at the same time. If you want to use N cores, say --cores N or -cN. For all cores on your system (be sure that this is appropriate) use --cores all. For no parallelization use --cores 1 or -c1.)
I then tried replacing with "snakemake --use-conda --conda-create-envs-only --cores 24" This seems to run as far as "Building DAG of jobs...
Creating conda environment src/snakefiles/hp.yml...
Downloading and installing remote packages."
Although this is taking rather a long time (> 5 minutes) so there may still be an issue.