Skip to content
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

libtinfo.so.6: no version information available (required by samtools) #32

Open
Sanrrone opened this issue Apr 15, 2024 · 0 comments
Open

Comments

@Sanrrone
Copy link

Dears,
Along with greeting you, I am running grid in the single mode and I am getting errors related with versions.
my log:

grid single -r HeP-1003_6_months_fq -e fastq.gz -o HeP-1003_grid_bb_complete -g /scratch/project_2007362/sandro/growingrate_test/idx/bifidobreve_dsm20213_complete.fna -n 4
Warning: [blastn] Examining 5 or more matches is recommended
Warning: [blastn] Number of threads was reduced to 40 to match the number of available CPUs
Warning: [blastn] Examining 5 or more matches is recommended
Warning: [blastn] Number of threads was reduced to 40 to match the number of available CPUs
3580912 reads; of these:
  3580912 (100.00%) were unpaired; of these:
    3580740 (100.00%) aligned 0 times
    4 (0.00%) aligned exactly 1 time
    168 (0.00%) aligned >1 times
0.00% overall alignment rate
141 reads; of these:
  141 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    4 (2.84%) aligned exactly 1 time
    137 (97.16%) aligned >1 times
100.00% overall alignment rate
144 reads; of these:
  144 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    1 (0.69%) aligned exactly 1 time
    143 (99.31%) aligned >1 times
100.00% overall alignment rate
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libtinfo.so.6: no version information available (required by samtools)
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libncurses.so.6: no version information available (required by samtools)
[samopen] SAM header is present: 1 sequences.
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libtinfo.so.6: no version information available (required by samtools)
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libtinfo.so.6: no version information available (required by samtools)
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libncurses.so.6: no version information available (required by samtools)
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libncurses.so.6: no version information available (required by samtools)
[bam_header_read] EOF marker is absent. The input is probably truncated.
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libtinfo.so.6: no version information available (required by samtools)
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libncurses.so.6: no version information available (required by samtools)
[samopen] SAM header is present: 1 sequences.
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libtinfo.so.6: no version information available (required by samtools)
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libncurses.so.6: no version information available (required by samtools)
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libtinfo.so.6: no version information available (required by samtools)
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libncurses.so.6: no version information available (required by samtools)
[bam_header_read] EOF marker is absent. The input is probably truncated.
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libtinfo.so.6: no version information available (required by samtools)
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libncurses.so.6: no version information available (required by samtools)
[samopen] SAM header is present: 1 sequences.
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libtinfo.so.6: no version information available (required by samtools)
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libncurses.so.6: no version information available (required by samtools)
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libtinfo.so.6: no version information available (required by samtools)
samtools: /scratch/project_2007362/software/mambaforge/envs/grid/bin/../lib/libncurses.so.6: no version information available (required by samtools)
[bam_header_read] EOF marker is absent. The input is probably truncated.
 
Attaching package: ‘dplyr’
 
The following objects are masked from ‘package:stats’:
 
    filter, lag
 
The following objects are masked from ‘package:base’:
 
    intersect, setdiff, setequal, union
 
Loading required package: proto
Warning message:
no DISPLAY variable so Tk is not available
`geom_smooth()` using formula = 'y ~ x'
Error in `filter()`:
ℹ In argument: `y == min(y)`.
Caused by error:
! object 'y' not found
Backtrace:
     ▆
  1. ├─filter(V, y == min(y)) %>% select(ymax)
  2. ├─dplyr::select(., ymax)
  3. ├─dplyr::filter(V, y == min(y))
  4. ├─dplyr:::filter.data.frame(V, y == min(y))
  5. │ └─dplyr:::filter_rows(.data, dots, by)
  6. │   └─dplyr:::filter_eval(...)
  7. │     ├─base::withCallingHandlers(...)
  8. │     └─mask$eval_all_filter(dots, env_filter)
  9. │       └─dplyr (local) eval()
 10. └─base::.handleSimpleError(`<fn>`, "object 'y' not found", base::quote(NULL))
 11.   └─dplyr (local) h(simpleError(msg, call))
 12.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted

also I am getting an
Error in `filter()`: ℹ In argument: `y == min(y)`. Caused by error: ! object 'y' not found error.

Is it okay even with the truncated bam? how can I fix it?.
thanks in advance!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant