Dear all,
I am running into this issue about Bowtie2 indexes and alignments. I am using standard settings and pipelines for analysis in several species that went fine so far, except for wheat where I am having this issue.
In the case the default settings of the bowtie2 index builder were not ok, I run bowtie2 again with these options: bowtie2-build GCA_025895885.1_ASM2589588v1_genomic.fa --noauto --large-index
But the issue with HiC-Pro stays.
Thank you!
Elena
bowtie2
Settings:
Output files: "bowtie2..bt2l"
Line rate: 7 (line is 128 bytes)
Lines per side: 1 (side is 128 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
GCA_025895885.1_ASM2589588v1_genomic.fa
Building a LARGE index
Reading reference sizes
Time reading reference sizes: 00:03:21
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:02:11
bmax according to bmaxDivN setting: 3664786976
Using parameters --bmax 2748590232 --dcv 1024
Doing ahead-of-time memory usage test
Dear all, I am running into this issue about Bowtie2 indexes and alignments. I am using standard settings and pipelines for analysis in several species that went fine so far, except for wheat where I am having this issue.
In the case the default settings of the bowtie2 index builder were not ok, I run bowtie2 again with these options: bowtie2-build GCA_025895885.1_ASM2589588v1_genomic.fa --noauto --large-index
But the issue with HiC-Pro stays.
Thank you! Elena
bowtie2 Settings: Output files: "bowtie2..bt2l" Line rate: 7 (line is 128 bytes) Lines per side: 1 (side is 128 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void:8, int:4, long:8, size_t:8 Input files DNA, FASTA: GCA_025895885.1_ASM2589588v1_genomic.fa Building a LARGE index Reading reference sizes Time reading reference sizes: 00:03:21 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:02:11 bmax according to bmaxDivN setting: 3664786976 Using parameters --bmax 2748590232 --dcv 1024 Doing ahead-of-time memory usage test
config-HiCPro_wheat.txt