Closed AnushkaChaturvedi closed 1 month ago
Usually, it comes from errors in the input file organization, or in the PAIR1_EXT / PAIR2_EXT
I checked the input file organization and the PAIR1_EXT / PAIR2__EXT both these things look fine. File organization- Rawdata
You were right the error was in input file organization. Thankyou so much.
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