Error in HiC-Pro 3.1.0 step1

[AnushkaChaturvedi]

Error in step1 of HiC-Pro

Run HiC-Pro 3.1.0

Tuesday 16 July 2024 10:06:51 AM IST Bowtie2 alignment step1 ... Logs: logs/1/mapping_step1.log [main_samview] fail to read the header from "-". Exit: Error in reads alignment - Exit make: *** [/home/angad/Vikash/HiC-Pro_3.1.0/bin/../scripts//Makefile:88: bowtie_global] Error 1

real 33m40.708s user 143m50.507s sys 2m14.070s

Command : time /home/angad/Vikash/HiC-Pro_3.1.0/bin/HiC-Pro -c /home/angad/Vikash/tools/Hic-Pro/Plant_test/config-hicpro.txt -i /home/angad/Vikash/tools/Hic-Pro/Plant_test/raw_data/qc_data/Sample_1/ -o hicproarabidop_test

Message in logs file

HiC-Pro mapping

stat: Bad file descriptor Warning: Could not open read file "rawdata/1/qc_SRR11149054_2.fastq" for reading; skipping... Error: No input read files were valid (ERR): bowtie2-align exited with value 1

[nservant]

Usually, it comes from errors in the input file organization, or in the PAIR1_EXT / PAIR2_EXT

[AnushkaChaturvedi]

I checked the input file organization and the PAIR1_EXT / PAIR2__EXT both these things look fine. File organization- Rawdata

• Sample_1
  • 1 -SRR_1.fastq
  • 2 -SRR_2.fastq

[AnushkaChaturvedi]

You were right the error was in input file organization. Thankyou so much.