snakemake question help

caiquanyou commented 4 years ago

when I Reproduce results as th page said by ran snakemake -prk and iget an error like this: Traceback (most recent call last): File "/root/test_cb_repro/Cell_BLAST/Evaluation/.snakemake/scripts/tmpjl7pf7be.dimension_reduction_metrics.py", line 54, in main() File "/root/test_cb_repro/Cell_BLAST/Evaluation/.snakemake/scripts/tmpjl7pf7be.dimension_reduction_metrics.py", line 36, in main y = y[~utils.na_mask(y)] AttributeError: module 'utils' has no attribute 'na_mask' How to fix and rerun?

Jeff1995 commented 4 years ago

Could you please verify that the na_mask function is defined in Evaluation/utils.py? (Should be in line 15 if you are using the latest version of the repo.)

If it is indeed defined, it is most likely caused by incorrect module being imported. Could you please insert a diagnostic line after the import section of Evaluations/dimension_reduction_metrics.py, like below:

import argparse
import json
import Cell_BLAST as cb
import utils
print(utils.__file__)  # Add this line

Rerun snakemake again and check the output?

caiquanyou commented 4 years ago

May work ，result below： /root/miniconda3/envs/cb-gpu/bin/python3.6 /root/test_cb_repro/Cell_BLAST/Evaluation/.snakemake/scripts/tmpeoigrv72.dimension_reduction_metrics.py /root/test_cb_repro/Cell_BLAST/Evaluation/utils.py [Thu Aug 27 11:27:04 2020] Finished job 4539. 7 of 10334 steps (0.07%) done

[Thu Aug 27 11:27:05 2020] rule dimension_reduction_metrics: input: ../Datasets/data/Bach/data.h5, ../Results/scPhere/Bach/dim_10/seed_4/result.h5 output: ../Results/scPhere/Bach/dim_10/seed_4/metrics.json jobid: 4530 reason: Missing output files: ../Results/scPhere/Bach/dim_10/seed_4/metrics.json wildcards: method=scPhere, dataset=Bach, dimensionality=10, seed=4

caiqy

------------------ 原始邮件 ------------------ 发件人: "gao-lab/Cell_BLAST" <notifications@github.com>; 发送时间: 2020年8月27日(星期四) 下午5:05 收件人: "gao-lab/Cell_BLAST"<Cell_BLAST@noreply.github.com>; 抄送: "xianmao"<951463554@qq.com>;"Author"<author@noreply.github.com>; 主题: Re: [gao-lab/Cell_BLAST] snakemake question help (#7)

Could you please verify that the na_mask function is defined in Evaluation/utils.py? (Should be in line 15 if you are using the latest version of the repo.)

If it is indeed defined, it is most likely caused by incorrect module being imported. Could you please insert a diagnostic line after the import section of "Evaluations/dimension_reduction_metrics.py", like below: import argparse import json import Cell_BLAST as cb import utils print(utils.file) # Add this line

Rerun snakemake again and check the output?

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Jeff1995 commented 4 years ago

If "/root/test_cb_repro/Cell_BLAST/Evaluation/utils.py" is the output of the diagnostic print statement, the imported module should be correct. So is the error about na_mask gone?

caiquanyou commented 4 years ago

I rewrite the relative imports and it may works for now

caiqy

------------------ 原始邮件 ------------------ 发件人: "gao-lab/Cell_BLAST" <notifications@github.com>; 发送时间: 2020年8月27日(星期四) 晚上7:40 收件人: "gao-lab/Cell_BLAST"<Cell_BLAST@noreply.github.com>; 抄送: "xianmao"<951463554@qq.com>;"Author"<author@noreply.github.com>; 主题: Re: [gao-lab/Cell_BLAST] snakemake question help (#7)

If "/root/test_cb_repro/Cell_BLAST/Evaluation/utils.py" is the output of the diagnostic print statement, the imported module should be correct. So is the error about na_mask gone?

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Jeff1995 commented 4 years ago

Okay great. Let me know if further issues were encountered.

gao-lab / Cell_BLAST

snakemake question help #7