Error when running make_bigwig_files.py

[li-sihan-lsh]

Hi,

I am a PhD student. I am following the eCLIP-Seq processing pipeline v2.0 20180724 and I am at the bigwig file generating step using make_bigwig_files.py. But I got the error report:

awk: line 2: function and never defined
awk: line 2: function and never defined
[main_samview] failed to write the SAM header
samtools view: error closing standard output: -1
needLargeMem: trying to allocate 0 bytes (limit: 100000000000)
awk: line 2: function and never defined
awk: line 2: function and never defined
[main_samview] failed to write the SAM header
samtools view: error closing standard output: -1
needLargeMem: trying to allocate 0 bytes (limit: 100000000000)

Based on "awk: line 2: function and never defined", I think the first error happened at line 16 in the script:
priming_call = "samtools view -h " + in_bam + " | awk 'BEGIN {OFS="\t"} {if(!!and($2,0x0080)) {if(!!and($2, 0x0004)) {$2 = $2 - 16} else {$2 = $2 + 16}}; print $0}' | samtools view -bS - | genomeCoverageBed -ibam stdin ".

Could you please help me check if is the code (!!and($2, 0x0080)) cause the problem? If yes, how can I modify or use this script?

Thank you very very much!
All the best!