bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

[Adeel]

Hi , 

I am trying to process HepG2 cell line ENCODE data using all 10 replicates (5 each from two replicates 1 and 2). I am running it in two separate jobs. Every time job terminates at bowtie_combine step. the error message is given below. 

mapping_combine.log is empty. 

Mon May  1 00:42:34 EDT 2023

Bowtie2 alignment step2 ...

Logs: logs/sample1/mapping_step2.log

Logs: logs/sample1/mapping_step2.log

Logs: logs/sample1/mapping_step2.log

Logs: logs/sample1/mapping_step2.log

Logs: logs/sample1/mapping_step2.log

--------------------------------------------

Wed May  3 04:40:55 EDT 2023

Combine R1/R2 alignment files ...

Logs: logs/sample1/mapping_combine.log

/usr/local/bin//HiC-Pro_3.1.0/scripts/bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

/usr/local/bin//HiC-Pro_3.1.0/scripts/bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

Logs: logs/sample1/mapping_combine.log

/usr/local/bin//HiC-Pro_3.1.0/scripts/bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

/usr/local/bin//HiC-Pro_3.1.0/scripts/bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

Logs: logs/sample1/mapping_combine.log

/usr/local/bin//HiC-Pro_3.1.0/scripts/bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

/usr/local/bin//HiC-Pro_3.1.0/scripts/bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

Logs: logs/sample1/mapping_combine.log

/usr/local/bin//HiC-Pro_3.1.0/scripts/bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

/usr/local/bin//HiC-Pro_3.1.0/scripts/bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

Logs: logs/sample1/mapping_combine.log

/usr/local/bin//HiC-Pro_3.1.0/scripts/bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

/usr/local/bin//HiC-Pro_3.1.0/scripts/bowtie_combine.sh: line 49: 768/ : syntax error: operand expected (error token is "/ ")

wishes, 

Adeel