The fix command fails halfway through execution, at Step 7. Error log:
=== Step 6: Analyze the report after REHAB ===
Going to sort the GWAS SS file by Chr and BP
Sorted by Chr and BP
Step 6 finished in 115.71317148208618 seconds
=== Step 7: REHAB: loopping through the GWAS SS file again and fixing entries ===
An error occured while looping through the SNPs file (see below)
An error occured on line 1 of the GWAS SS file (see below)
Traceback (most recent call last):
File "/usr/local/bin/SumStatsRehab", line 11, in <module> load_entry_point('SumStatsRehab==1.1.2', 'console_scripts', 'SumStatsRehab')()
File "/usr/local/lib/python3.8/dist-packages/SumStatsRehab-1.1.2-py3.8.egg/SumStatsRehab.py", line 722, in main fix(args.INPUT_GWAS_FILE, args.OUTPUT_FILE,
File "/usr/local/lib/python3.8/dist-packages/SumStatsRehab-1.1.2-py3.8.egg/SumStatsRehab.py", line 437, in fix loop_fix(
File "/usr/local/lib/python3.8/dist-packages/SumStatsRehab-1.1.2-py3.8.egg/lib/loop_fix.py", line 813, in loop_fix raise e
File "/usr/local/lib/python3.8/dist-packages/SumStatsRehab-1.1.2-py3.8.egg/lib/loop_fix.py", line 804, in loop_fix run_all(resolvers, fields, resolvers_args)
File "/usr/local/lib/python3.8/dist-packages/SumStatsRehab-1.1.2-py3.8.egg/lib/loop_fix.py", line 696, in run_all resolvers[res_i](fields, *args[res_i])
File "/usr/local/lib/python3.8/dist-packages/SumStatsRehab-1.1.2-py3.8.egg/lib/loop_fix.py", line 616, in resolve_rsID raise e
File "/usr/local/lib/python3.8/dist-packages/SumStatsRehab-1.1.2-py3.8.egg/lib/loop_fix.py", line 589, in resolve_rsID chr_snps, bp_snps, rsid, ref, alt, freq = read_dbSNP1_data_row(SNPs_FILE_o)
File "/usr/local/lib/python3.8/dist-packages/SumStatsRehab-1.1.2-py3.8.egg/lib/loop_fix.py", line 253, in read_dbSNP1_data_row int(words[1]), # BP
ValueError: invalid literal for int() with base 10: 'ID'
The fix command fails halfway through execution, at Step 7. Error log:
Reported by Mahantesh B