TypeError: can only concatenate str (not "NoneType") to str
Closed this issue · 9 comments
I am running a test using the example .bam and .fna files provided using the following shell scripting on an M1 Mac:
MicrobeMod call_methylation -b ./tests/test_data/test.bam -r ./tests/test_data/EcoliCVM05_GCF_000005845.2_ASM584v2_genomic.fna -t 10
However, I am getting the following error when it's running:
Traceback (most recent call last):
File "/Users/johnbeckley/miniconda3/envs/microbemod/bin/MicrobeMod", line 173, in
microbemod.main(
File "/Users/johnbeckley/miniconda3/envs/microbemod/lib/python3.8/site-packages/MicrobeMod/microbemod.py", line 558, in main
modkit_table_tmp = assign_motifs(
File "/Users/johnbeckley/miniconda3/envs/microbemod/lib/python3.8/site-packages/MicrobeMod/microbemod.py", line 325, in assign_motifs
"Found and trimmed motif: "
TypeError: can only concatenate str (not "NoneType") to str
I also had this error with aws downloaded data. Any idea what the issue is here?
Bit hard to figure out what's going on here from this.
- Can you check these dependencies?
streme --version
modkit --version
-
Does this error occur on the m5c or m6a stage?
-
What do your
test_low.bedandtest_m_pos_streme/streme.txtlook like?
Here are the dependency versions:
(microbemod) johnbeckley@Johns-MBP-10 MicrobeMod % streme --version
modkit --version
5.4.1
mod_kit 0.2.4
This is the furthest I get:
24-03-10 15:16:52 INFO Running modkit: modkit pileup -t 10 ./tests/test_data/test.bam test_low.bed -r ./tests/test_data/EcoliCVM05_GCF_000005845.2_ASM584v2_genomic.fna --only-tabs --filter-threshold 0.66
24-03-10 15:16:57 INFO Reading Modkit table...
24-03-10 15:16:58 INFO Retrieving sequences
24-03-10 15:16:58 INFO Total number of sites with any possible calls (including low quality): 116243 bases
24-03-10 15:16:58 INFO Median coverage (stranded): 53.0x
24-03-10 15:16:58 INFO Total number of sites with greater than min coverage (10x): 80836 bases
24-03-10 15:16:58 INFO Potential sites (>33%) for methylation type m: 573 bases
24-03-10 15:16:58 INFO High quality sites (>66%) for methylation type m: 421 bases
24-03-10 15:16:58 INFO Very high quality sites (>90%) for methylation type m: 348 bases
24-03-10 15:16:58 INFO Potential sites (>33%) for methylation type a: 1596 bases
24-03-10 15:16:58 INFO High quality sites (>66%) for methylation type a: 845 bases
24-03-10 15:16:58 INFO Very high quality sites (>90%) for methylation type a: 510 bases
24-03-10 15:16:58 INFO Running for Methylation type: 6mA
24-03-10 15:16:58 INFO Modkit table size: 57110
24-03-10 15:16:58 INFO 510 sites for STREME with cutoff 0.9 and min coverage 10
24-03-10 15:16:58 INFO Creating background control distribution: test_a_control.fasta
24-03-10 15:16:58 INFO Running STREME: streme . --n test_a_control.fasta -p test_a_pos.fasta -o test_a_pos_streme
So I assume this means that 6mA stage?
For the files:
Want to try an update to streme 5.5 and see if that fixes it?
Can you send the streme.xml as well?
Will try to do streme 5.5, but have been having trouble updating. Working on it.
Oh this definitely seems like a streme version. However, I think we can modify it to support older versions of streme.
Would you be able to test it out? In microbemod.py can you change this line (330):
motif.get("npassing")
to
motif.get("total_sites")
And then run pip install . again and give that a try? If that fixes your issue, I'll release a new version with that fix.
It worked! Thanks a lot for your help. That was the only streme version that I was able to install with conda.
Hi,
I am getting the same error using the test dataset with microbemod v1.0.3, but with streme version 5.5.2 installed
streme.txt says "Stopped because the last motif found had no valid sites."
24-04-08 07:13:20 INFO Running modkit: modkit pileup -t 10 test.bam test_low.bed -r EcoliCVM05_GCF_000005845.2_ASM584v2_genomic.fna --only-tabs --filter-threshold 0.66
24-04-08 07:13:27 INFO Reading Modkit table...
24-04-08 07:13:28 INFO Retrieving sequences
24-04-08 07:13:28 INFO Total number of sites with any possible calls (including low quality): 116243 bases
24-04-08 07:13:28 INFO Median coverage (stranded): 53.0x
24-04-08 07:13:28 INFO Total number of sites with greater than min coverage (10x): 80836 bases
24-04-08 07:13:28 INFO Potential sites (>33%) for methylation type m: 573 bases
24-04-08 07:13:28 INFO High quality sites (>66%) for methylation type m: 421 bases
24-04-08 07:13:28 INFO Very high quality sites (>90%) for methylation type m: 348 bases
24-04-08 07:13:28 INFO Potential sites (>33%) for methylation type a: 1596 bases
24-04-08 07:13:28 INFO High quality sites (>66%) for methylation type a: 845 bases
24-04-08 07:13:28 INFO Very high quality sites (>90%) for methylation type a: 510 bases
24-04-08 07:13:28 INFO Running for Methylation type: 6mA
24-04-08 07:13:28 INFO Modkit table size: 57110
24-04-08 07:13:28 INFO 510 sites for STREME with cutoff 0.9 and min coverage 10
24-04-08 07:13:28 INFO Creating background control distribution: test_a_control.fasta
24-04-08 07:13:28 INFO Running STREME: streme . --n test_a_control.fasta -p test_a_pos.fasta -o test_a_pos_streme
Traceback (most recent call last):
Traceback (most recent call last):
File "/home/ubuntu/scratch/software/miniforge3/envs/microbemod/bin/MicrobeMod", line 173, in
microbemod.main(
File "/home/ubuntu/scratch/software/miniforge3/envs/microbemod/lib/python3.10/site-packages/MicrobeMod/microbemod.py", line 558, in main
modkit_table_tmp = assign_motifs(
File "/home/ubuntu/scratch/software/miniforge3/envs/microbemod/lib/python3.10/site-packages/MicrobeMod/microbemod.py", line 325, in assign_motifs
"Found and trimmed motif: "
TypeError: can only concatenate str (not "NoneType") to str
Changing motif.get("npassing") to total_sites works for me as well
However due to git everytime i run pip install . it reverts to the remote version but I've got it working
Will try to release an update soon!
fixed in #26