Entering edit mode
7 months ago
Atul K.
•
0
Why I am getting this error when I have my hisat2 indexed genome is in the desired folder and th path to the folder is correct.
While running the ciriquant i am getting this error i.e.
CIRIquant --config /home/akk/circ_analysis/new_analysis/config.yaml -1 /home/akk/circ_analysis/new_analysis/SRR_1.fastq -2 /home/akk/circ_analysis/new_analysis/SRR_2.fastq
Traceback (most recent call last):
File "/home/akk/software_library/CIRIquant_env/bin/CIRIquant", line 8, in <module>
sys.exit(main())
File "/home/akk/software_library/CIRIquant_env/lib/python2.7/site-packages/CIRIquant/main.py", line 97, in main
config = check_config(check_file(args.config_file))
File "/home/akk/software_library/CIRIquant_env/lib/python2.7/site-packages/CIRIquant/utils.py", line 115, in check_config
raise ConfigError('Could not find hisat2 index with suffix: *.[1-8].ht2 or *.[1-8].ht2l, please check your configuration')
CIRIquant.utils.ConfigError: Could not find hisat2 index with suffix: *.[1-8].ht2 or *.[1-8].ht2l, please check your configuration
the config file i am using is as follows :
# configuration for CIRIquant
# Input files
read1: /home/akk/circ_analysis/new_analysis/SRR_1.fastq
read2: /home/akk/circ_analysis/new_analysis/SRR_2.fastq
# Output directory
output_dir: ./
# Prefix for output files
output_prefix: prefix_for_output_files
# Paths to tools
tools:
bwa: /home/akk/software_library/CIRIquant_env/bin/bwa
hisat2: /home/akk/software_library/CIRIquant_env/bin/hisat2
stringtie: /home/akk/software_library/CIRIquant_env/bin/stringtie
samtools: /home/akk/software_library/CIRIquant_env/bin/samtools
# Paths to reference files
reference:
fasta: /home/akk/hg38_genome/hg38.fa
gtf: /home/akk/hg38_genome/hg38.refGene.gtf
bwa_index: /home/akk/hg38_genome/hg38/hg38
hisat_index: /home/akk/hg38_genome/hg38hisat
# Other parameters
threads: 4
anchor: 5
library_type: 0
And the contents of the folder hg38hisat are as follows:
akk@kashyap:~/hg38_genome/hg38hisat$ ls -lash
total 4.4G
4.0K drwxrwxr-x 2 akk akk 4.0K Apr 10 16:42 .
4.0K drwxrwxr-x 6 akk akk 4.0K Apr 10 15:05 ..
974M -rw-rw-r-- 1 akk akk 974M Apr 10 16:42 hg38.1.ht2
728M -rw-rw-r-- 1 akk akk 728M Apr 10 16:42 hg38.2.ht2
16K -rw-rw-r-- 1 akk akk 15K Apr 10 15:41 hg38.3.ht2
728M -rw-rw-r-- 1 akk akk 728M Apr 10 15:41 hg38.4.ht2
1.3G -rw-rw-r-- 1 akk akk 1.3G Apr 10 16:49 hg38.5.ht2
741M -rw-rw-r-- 1 akk akk 741M Apr 10 16:49 hg38.6.ht2
4.0K -rw-rw-r-- 1 akk akk 12 Apr 10 15:41 hg38.7.ht2
4.0K -rw-rw-r-- 1 akk akk 8 Apr 10 15:41 hg38.8.ht2
It is pretty clear to me that the path to hisat2 indexed genome is correct but i do not know why it is not able to find it. Please help, i am missing something very basic ??
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the job so I suggest trying that.
Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but the following error came :
Looks like the bam file pysam is trying to read is not properly formated. I don't know if it is a bug from CIRI2 or something else. Perhaps you could try asking a separate question on the forum. See also similar errors: pysam alignment error and pysam error when reading .bam file ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format?
Thank you.