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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!
The text was updated successfully, but these errors were encountered:
Dears,
Along with greeting you, I am running grid in the single mode and I am getting errors related with versions.
my log:
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!
The text was updated successfully, but these errors were encountered: