error when using croo to generate report

[yr-gh]

Hello, I'm trying to generate ENCODE rna-seq-peipe report by croo, bu I met some problems.

The Comwell has printed that the pipeline has been run successfully, and the metadata.json file has beed generated.

But it still raised a bug when I used croo to generate a report.

The attachments are debug info file and metadata.json file.

thank you for helpful advice!
croo.log
metadata.json.log

[byee4]

Hi, I am hitting this error now as well using the dev branch. Could be related to? ENCODE-DCC/croo#13

[wangxiangxiu]

@yr-gh Hello, have you fixed this problem? It present similar issue when using croo to generate RNA-seq pipeline output.

[yr-gh]

@wangxiangxiu not yet, this problem seems occurring when generating report from MAplot.png, so when i run only with two replicates i delete MAplot-related (mad_qc in metadata.json) fields from metadata.json, then i re-run croo on the revised metadata.json. because i found there is no such problem when run with greater than 2 replicates (when you have more than 2 replicates, it seems not to run the mad_qc.py, so there is no error occurred).

[yr-gh]

@wangxiangxiu here is the py script i use to del mad_qc-related fields from metadata.json

del_mad_qc.py -j metadat.json -o revised_metadata.json

then re-run revised_metadata.json using croo again

if you have a better solution about this problem, please let me know, thank you

#!/usr/bin/env python

'''
Delete the mad_qc-related fileds, because croo cannot work correctly for some reason, if mad_qc is run.
The only way that I can solve the bug is to delete the mad_qc-related filed.
'''

import json
import argparse

def parse_arguments():
parser = argparse.ArgumentParser(description = 'Delete mad_qc-related fields from metadata.json.')
parser.add_argument('-j', '--json', metavar = 'JSON', type = str, required = True, help = 'input metadata.json file')
parser.add_argument('-o', '--out_file', metavar = 'JSON', type = str, required = True, help = 'output revised metadata.json file')
args = parser.parse_args()
return args

def main():
print('Start deleting ...')

args = parse_arguments()

with open(args.json, 'r') as ijf:
    ijf_content = json.load(ijf)

# delete mad_qc-related fields
del ijf_content['calls']['rna.mad_qc']
del ijf_content['outputs']['rna.mad_qc.madQCmetrics']
del ijf_content['outputs']['rna.mad_qc.python_log']
del ijf_content['outputs']['rna.mad_qc.madQCplot']
del ijf_content['inputs']['mad_qc_disk']

with open(args.out_file, 'w') as ojf:
    json.dump(ijf_content, ojf, sort_keys = False, indent = 4)

print('Delete done!')

if name == 'main':
main()