ValueError: could not convert string to float: 'start'

[weizhousjtu]

Traceback (most recent call last): File "/home/anaconda3/bin/comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.2', 'comb-p') File "/home/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1446, in run_script exec(code, namespace, namespace) File "/home/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 39, in main() File "/home/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 36, in main module.main() File "/home/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 77, in main use_fdr=not args.no_fdr) File "/home/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 89, in pipeline step = min(acf_dist, stepsize.stepsize(bed_files, col_num)) File "/home/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/stepsize.py", line 19, in stepsize L = list(chromlist) File "/home/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/_common.py", line 64, in bediter start = int(float(l[1])) ValueError: could not convert string to float: 'start'

I installed the latest version but still wrong, does anyone could help me?

[brentp]

hi, you can add a '#' to the start of your header line so that comb-p knows it's a header.

[weizhousjtu]

thank you！ I add a '#' to the start of header line, it worked. however, another error occured. `comb-p pipeline -c 4 --seed 0.01 --dist 500 --region-filter-p 0.01 \

-p ./ --annotate hg19 cgInfor_combp_final_sort.bed setting --acf-dist to 0.33 * --dist == 170 calculated stepsize as: 170 ACF: #lag_min lag_max correlation N p 1 171 0.1543 115308 0 wrote: ./.acf.txt

original lambda: 1.38

wrote: ./.slk.bed.gz with lambda: 1.42 wrote: ./.fdr.bed.gz wrote: ./.regions.bed.gz (14 regions)

read 14 regions from ./.regions.bed.gz

calculating ACF out to: 166

with 2 lags: [1, 171]

Done with one-time ACF calculation

361348 bases used as coverage for sidak correction "warning: 0-length region found. does input have 0-length intervals? using length of 1 and not reporting further 0-length intervalswrote: ./.regions-p.bed.gz, (regions with corrected-p < 0.05: 7) Traceback (most recent call last): File "/home/anaconda3/bin/comb-p", line 4, in import('pkg_resources').run_script('cpv==0.50.2', 'comb-p') File "/home/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1446, in run_script exec(code, namespace, namespace) File "/home/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 39, in main() File "/home/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/EGG-INFO/scripts/comb-p", line 36, in main module.main() File "/home/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 77, in main use_fdr=not args.no_fdr) File "/home/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/pipeline.py", line 183, in pipeline regions_bed, p_col_name=col_num)): File "/home/anaconda3/lib/python3.7/site-packages/cpv-0.50.2-py3.7.egg/cpv/filter.py", line 73, in filter raise Exception('need header in p-value file to run filter') Exception: need header in p-value file to run filter`

[brentp]

can you show the output of head -1 cgInfor_combp_final_sort.bed

[weizhousjtu]

head -1 cgInfor_combp_final_sort.bed chr1 10850 10850 0.805014817073095 0.247123295906677 it seems the header line is missing after run the script upon

[brentp]

no. comb-p doesn't alter the original file, you gave it a file without a header and/or you sorted the header to somewhere other than the first line of the file.

[weizhousjtu]

yes, I must sorted first and add the header line. thank you for your explain!