BOL: All site questions

bowtie2-align-s: error while loading shared libraries

Abhi — Fri, 17 Dec 2021 05:35:47 -0600

/home/emilyw/.conda/envs/shotgun_134/bin/bowtie2-align-s: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory (ERR): Description of arguments failed! Exiting now ...

How to resolve this ?

Palgoin installation return this warning ?

Abhi — Mon, 15 Nov 2021 23:43:03 -0600

For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
mpiexec --mca opal_cuda_support 1 ...
In addition, the UCX support is also built but disabled by default.
To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment
variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
Equivalently, you can set the MCA parameters in the command line:
mpiexec --mca pml ucx --mca osc ucx ...
Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX.
Please consult UCX's documentation for detail.

Rasflow Error: Directory cannot be locked

Neel — Mon, 06 Sep 2021 06:45:10 -0500

Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory:
/home/RASflow
If you are sure that no other instances of snakemake are running on this directory, the remaining lock was likely caused by a kill signal or a power loss. It can be removed with the --unlock argument.

How to get the container id ?

BioStar — Mon, 23 Aug 2021 18:57:53 -0500

What are difference between Unique and Distinct K-mers ?

Shruti Paniwala — Wed, 18 Aug 2021 08:41:07 -0500

How to resolve samtools index error "Chromosome blocks not continuous" ?

LEGE — Thu, 12 Aug 2021 08:53:42 -0500

samtools index mappedPairs.sorted.bam return the following error ...

[bam_sort_core] merging from 0 files and 2 in-memory blocks...
[E::hts_idx_push] Chromosome blocks not continuous
samtools index: failed to create index for "mappedPairs.sorted.bam"

What is chastity ?

Surabhi Chaudhary — Fri, 25 Jun 2021 04:56:32 -0500

While working with illumina data, I came cross chastity filter. I am wondering about it !

GLIBC_2.23' not found error with alienomics !

LEGE — Tue, 23 Mar 2021 07:38:33 -0500

(base) lege@Bathymodiolus:~$ ./alienomics_v0.3.1
Can't load '/tmp/par-6a6974656e647261/cache-f3e57c2becbb7e00629c1273cf03dd05ad45721b/5b8c5ac2.so' for module POSIX: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.23' not found (required by /tmp/par-6a6974656e647261/cache-f3e57c2becbb7e00629c1273cf03dd05ad45721b/5b8c5ac2.so) at /usr/lib/x86_64-linux-gnu/perl/5.26/DynaLoader.pm line 187.
at /usr/local/share/perl/5.26.1/PAR/Heavy.pm line 140.
Compilation failed in require at script/alienomics_v0.3.pl line 28.
BEGIN failed--compilation aborted at script/alienomics_v0.3.pl line 28.

How to fiv "Error in library(reshape) : there is no package called ‘reshape’"

Rahul Nayak — Sun, 14 Mar 2021 10:02:43 -0500

[main] Real time: 2.026 sec; CPU: 1.798 sec
Plotting the coverage
Error in library(reshape) : there is no package called ‘reshape’
Execution halted
./setu.sh -k yes -m pe -t 1 -r SRR11140750_1.fastq.gz,SRR11140750_2.fastq.gz 11,91s user 1,30s system 125% cpu 10,533 total

Where is Bio::SeqIO installed in my Linux system ?

LEGE — Wed, 17 Feb 2021 22:11:57 -0600

How to find the location of the module installed