which version of reference fasta file are suitable for reditools2.0?

[lizhan96]

dear developer

I ran reditools by the following code, and got error messages about the reference.

1. ucsc reference file was supplying
   python /data_6t/lizhan/02.software/REDItools/reditools2.0-master/src/cineca/reditools.py -f T154.bam -r /data_6t/lizhan/database/genome/human/ucsc/hg38/hg38.fa -o ./edit4

Traceback (most recent call last):
File "/data_6t/lizhan/02.software/REDItools/reditools2.0-master/src/cineca/reditools.py", line 984, in analyze
chr_ref = reference_reader.fetch(read.reference_name)
File "pysam/libcfaidx.pyx", line 303, in pysam.libcfaidx.FastaFile.fetch
KeyError: "sequence 'KQ759759.1' not present"

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/data_6t/lizhan/02.software/REDItools/reditools2.0-master/src/cineca/reditools.py", line 1374, in
analyze(options)
File "/data_6t/lizhan/02.software/REDItools/reditools2.0-master/src/cineca/reditools.py", line 986, in analyze
chr_ref = reference_reader.fetch("chr" + read.reference_name)
File "pysam/libcfaidx.pyx", line 303, in pysam.libcfaidx.FastaFile.fetch
KeyError: "sequence 'chrKQ759759.1' not present"

then I grep KQ759759.1 with the ref file

$grep KQ759759.1 /data_6t/lizhan/database/genome/human/ucsc/hg38/hg38.fa

chr11_KQ759759v1_fix

2. ensemble reference file was supplying
   python /data_6t/lizhan/02.software/REDItools/reditools2.0-master/src/cineca/reditools.py -f T154.bam -r /data_6t/lizhan/database/reditools_index/Homo_sapiens.GRCh38.dna.primary_assembly.fa -o ./edit3

error message

Traceback (most recent call last):
File "/data_6t/lizhan/02.software/REDItools/reditools2.0-master/src/cineca/reditools.py", line 984, in analyze
chr_ref = reference_reader.fetch(read.reference_name)
File "pysam/libcfaidx.pyx", line 303, in pysam.libcfaidx.FastaFile.fetch
KeyError: "sequence 'KQ759759.1' not present"

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/data_6t/lizhan/02.software/REDItools/reditools2.0-master/src/cineca/reditools.py", line 1374, in
analyze(options)
File "/data_6t/lizhan/02.software/REDItools/reditools2.0-master/src/cineca/reditools.py", line 986, in analyze
chr_ref = reference_reader.fetch("chr" + read.reference_name)
File "pysam/libcfaidx.pyx", line 303, in pysam.libcfaidx.FastaFile.fetch
KeyError: "sequence 'chrKQ759759.1' not present"