-
Notifications
You must be signed in to change notification settings - Fork 85
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
line 8: 110334 Aborted(core dumped) #642
Comments
@yao-chenxin Sorry for the late reply. I feel like the issue might be caused by non-ACGT base pairs within input HiFi reads. |
How to solve this error? |
hi,
I checked and found that there was an incomplete fastq file, re-generated fastq with bam2fastq, and then fixed the problem.
Best wishes!
在 2024-07-23 08:27:15,"Chuan Dong" ***@***.***> 写道:
How to solve this error?
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you were mentioned.Message ID: ***@***.***>
|
Thank you for your kind response. |
Hello, I have a hypermemory problem:
The error message is as follows:
[M::ha_hist_line] rest: ******************************************************************************************> 50214823
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_ft_gen] peak_hom: 53; peak_het: -1
[M::ha_ct_shrink::20212.2275.86] ==> counted 73802001 distinct minimizer k-mers
[M::ha_ft_gen::20288.5855.84@59.941GB] ==> filtered out 73802001 k-mers occurring 265 or more times
[M::ha_opt_update_cov] updated max_n_chain to 265
[M::yak_count] collected 1223402570 minimizers
[M::yak_count] collected 1637002108 minimizers
[M::yak_count] collected 439807275 minimizers
[M::yak_count] collected 1693570594 minimizers
[M::yak_count] collected 434857897 minimizers
[M::yak_count] collected 182925201 minimizers
hifiasm: sketch.cpp:581: void mz1_ha_sketch(const char, int, int, int, uint32_t, int, ha_mz1_v, const void, int, kvec_t_u8_warp, kvec_t_u64_warp, ha_pt_t, int, int32_t, float, st_mt_t, int32_t, int32_t, void): Assertion
len > 0 && (int64_t)(len) < (int64_t)((((uint64_t)1)<<27)) && (int64_t)(rid) < (int64_t)((((uint64_t)1)<<28)) && (w > 0 && w < 256) && (k > 0 && k <= 63)' failed. /opt/ge2011.11/default/spool/compute01/job_scripts/2912: line 8: 110334 Aborted (core dumped) /software/hifiasm-0.19.8/hifiasm -o $spe -t 20 --hom-cov 53
ls *.fasta.gz`ERROR: failed to read the graph
no sca
ERROR: failed to read the graph
My memory is given 1.5T (vg=1.5T,p=35),still can't solve;
Could you please take a look? Is there any good solution.(The genome is 9 g)(--hg-size 9g)
Thank you very much!
The text was updated successfully, but these errors were encountered: