Docker container?

[R-Najjar]

Hello, Is there a docker container for TElocal?

Thank you

[olivertam]

Hi,

Thank you for your interest in the software. Currently, there is no Docker container for TElocal. We can look into adding one.

Thanks.

[olivertam]

Could you try this and let us know if it works?

docker pull mhammelllab/telocal

[R-Najjar]

Hi Oliver, Thank you very much for the quick response. I tested it and I get one warning message (see below), but it seems to work fine. I don't get this warning message when I use the TEtranscripts container. I use apptainer (singularity)

Best, Rayan

/usr/local/bin/TElocal:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').run_script('TElocal==1.1.1', 'TElocal')
INFO  @ Thu, 18 Apr 2024 00:03:58: 
ARGUMENTS LIST:
name = /gscratch/sine/local_multi_sorted6216.bam
BAM file = sorted6216.bam
GTF file = /gscratch/gencode.v42.primary_assembly.annotation.gtf 
TE file = /gscratch/tools/GRCm38_GENCODE_rmsk_TE.gtf.locInd 
multi-mapper mode = multi 
stranded = reverse 
number of iteration = 100
Alignments grouped by read ID = False

INFO  @ Thu, 18 Apr 2024 00:03:58: Processing annotation files ...

INFO  @ Thu, 18 Apr 2024 00:03:58: Building gene index ....... 

100000 GTF lines processed.
[removed processing lines here]
1600000 GTF lines processed.
INFO  @ Thu, 18 Apr 2024 00:28:48: Done building gene index ...... 

INFO  @ Thu, 18 Apr 2024 00:28:48: Attempting to load TE index ...... 

INFO  @ Thu, 18 Apr 2024 00:29:06: TE index loaded ...... 

INFO  @ Thu, 18 Apr 2024 00:29:06: 
Reading sample file ... 

1000000 alignments  processed.
[removed processing lines here]
66000000 alignments  processed.
uniq te counts = 1709783.0000000002 
.......start iterative optimization ..........
multi-reads = 438629 SQUAREM iteraton [1]
num of multi reads = 438629
total multi counts = 438495.9999999991
num of multi reads = 438629
total multi counts = 438496.0000000037
alpha = 1.0, SQUAREM iteraton [2]
num of multi reads = 438629
total multi counts = 438495.99999999395
num of multi reads = 438629
total multi counts = 438496.00000000116
alpha = 1.3093553717170463.
 Performing a stabilization step.
num of multi reads = 438629
total multi counts = 438496.0000000026
alpha = 1.3093553717170463, SQUAREM iteraton [3]
num of multi reads = 438629
total multi counts = 438496.0000000015
num of multi reads = 438629
total multi counts = 438495.99999999686
alpha = 1.9690161121534757.
 Performing a stabilization step.
num of multi reads = 438629
total multi counts = 438495.9999999955
alpha = 1.9690161121534757, SQUAREM iteraton [4]
num of multi reads = 438629
total multi counts = 438496.00000000343
num of multi reads = 438629
total multi counts = 438495.9999999946
rNome < OPT_TOL 
converge at iteration 4
num of multi reads = 438629
TE counts total 2148279.0000000037
Gene counts total 44574590.687064946

In library sorted6216.bam:
Total annotated reads = 46722869.687064946
Total non-uniquely mapped reads = 7084187
Total unannotated reads = 2225902

INFO  @ Thu, 18 Apr 2024 01:03:42: Finished processing sample file 

[olivertam]

Hi,

I think this is because the current Docker installed TElocal from setup.py, versus using pip to install. However, looking at the log, it appears to have completed successfully. Could you check that the output count table is present? If so, I might ignore that warning message.

Thanks.

[R-Najjar]

Yes, the output table is present. Thank you again for creating the container so quickly.