Random error
Closed this issue · 4 comments
Hi there,
I just started using mcclintock and have run into some issues.
Here it is:
Command:
python3 ~/bin/mcclintock/mcclintock.py \\
-r ${params.genome} \\
-c ${params.con_seqs} \\
-g ${params.ref_locs} \\
-t ${params.families} \\
-1 ${fq1} \\
-2 ${fq2} \\
-p ${task.cpus} \\
-m ngs_te_mapper,temp,retroseq,te-locate \\
-o mcclintock_out
Error:
Traceback (most recent call last):
File "/projects/b1042/AndersenLab/work/stefan/ca/ff5ae5af5922d73544acee2c85de68/mcclintock_out/snakemake/1096582/.snakemake/scripts/tmpx20ygtgw.temp_post.py", line 154, in <module>
main()
File "/projects/b1042/AndersenLab/work/stefan/ca/ff5ae5af5922d73544acee2c85de68/mcclintock_out/snakemake/1096582/.snakemake/scripts/tmpx20ygtgw.temp_post.py", line 29, in main
mccutils.make_nonredundant_bed(insertions, sample_name, out_dir, method="temp")
File "/home/szs315/bin/mcclintock/scripts/mccutils.py", line 394, in make_nonredundant_bed
if uniq_inserts[key].temp.support != "!" and insert.temp.support > uniq_inserts[key].temp.support:
TypeError: '>' not supported between instances of 'str' and 'float'
[Thu Jul 30 12:16:40 2020]
Error in rule process_temp:
jobid: 0
output: /projects/b1042/AndersenLab/work/stefan/ca/ff5ae5af5922d73544acee2c85de68/mcclintock_out/results/TEMP/BGI2-RET6-JU1440-trim-1P_temp_redundant.bed, /projects/b1042/AndersenLab/work/stefan/ca/ff5ae5af5922d73544acee2c85de68/mcclintock_out/results/TEMP/BGI2-RET6-JU1440-trim-1P_temp_nonredundant.bed
conda-env: /home/szs315/bin/mcclintock/install/envs/conda/716bd1a3
RuleException:
CalledProcessError in line 498 of /projects/b1042/AndersenLab/work/stefan/ca/ff5ae5af5922d73544acee2c85de68/mcclintock_out/snakemake/1096582/Snakefile:
Command 'source /home/szs315/.pyenv/versions/miniconda3-4.3.27/bin/activate '/home/szs315/bin/mcclintock/install/envs/conda/716bd1a3'; set -euo pipefail; /home/szs315/.pyenv/versions/miniconda3-4.3.27/envs/mcclintock/bin/python3.8 /projects/b1042/AndersenLab/work/stefan/ca/ff5ae5af5922d73544acee2c85de68/mcclintock_out/snakemake/1096582/.snakemake/scripts/tmpx20ygtgw.temp_post.py' returned non-zero exit status 1.
File "/projects/b1042/AndersenLab/work/stefan/ca/ff5ae5af5922d73544acee2c85de68/mcclintock_out/snakemake/1096582/Snakefile", line 498, in __rule_process_temp
File "/home/szs315/.pyenv/versions/miniconda3-4.3.27/envs/mcclintock/lib/python3.8/concurrent/futures/thread.py", line 57, in run
Exiting because a job execution failed. Look above for error message
I understand this is not the most useful error post, but I am running about a 1000 samples and decided to show you the error in case it makes sense to you. In the mean time, I am just skipping the sample that caused the issue.
Best
@Thatguy027 Thanks for opening this issue.
I've seen this error before and currently have fixed it on the TEPID branch. I'll merge these changes with master soon once I've tested that it is working as intended.
oh great - there are some other weird errors i was getting with popoolation2 as well, but did not save them. if i can dig them up, i'll post another random error post.
thanks for the quick response!
on a side note - is there a way to pre-configure the TE caller parameters?
- Each component method has associated config files that can be modified to change parameters under
path/to/mcclintock/config/${method}/. For example, the popoolationTE2 run config file is: https://github.com/bergmanlab/mcclintock/blob/master/config/popoolationte2/popoolationte2_run.py - I have been testing everything using the default parameters so if you run into any issues when modifying the config files, please feel free to open an issue about it
excellent, thank you very much!