Error in absent module

[JBerthelier]

Hello,

I think I have sucessfully installed TEMP2.
The test dataset works fine for the modules "insertion" and "insertion2".

However, I got this error for the module "absent" :

---

Can't open test.excision.cluster.rpmk.refined.bp.sfcp since No such file or directory
[main_samview] region "Chr:1-505" specifies an invalid region or unknown reference. Continue anyway.
[main_samview] region "Chr:1-503" specifies an invalid region or unknown reference. Continue anyway.
[main_samview] region "Chr:1-505" specifies an invalid region or unknown reference. Continue anyway.
[main_samview] region "Chr:1-503" specifies an invalid region or unknown reference. Continue anyway.
Illegal division by zero at /home2020/home/uha/jberthel/Tools/TEMP/TEMP2/bin/summarize_excision.pl line 45, line 1.

---

In the output directory, my output data are :

ls -l
total 18253
-rw-r--r-- 1 user 0 Jun 26 11:13 temp
-rw-r--r-- 1 user 0 Jun 26 11:13 temp2
-rw-r--r-- 1 user 243 Jun 26 10:58 test.absence.refined.bp.summary
-rw-r--r-- 1 user 0 Jun 26 10:49 test.excision.cluster.rpmk
-rw-r--r-- 1 user 159 Jun 26 10:58 test.excision.cluster.rpmk.refined.bp
-rw-r--r-- 1 user 110 Jun 26 10:58 test.excision.cluster.rpmk.refined.bp.refsup
-rw-r--r-- 1 user 0 Jun 26 10:49 test.excision.cluster.rpmk.sfcp
-rw-r--r-- 1 user 18266429 Jun 26 10:49 test.sorted.bam
-rw-r--r-- 1 user 17768 Jun 26 10:49 test.sorted.bam.bai
-rw-r--r-- 1 user 404880 Jun 26 10:49 test.unpair.sam

Could you help me to understand the cause ?

I used the dataset provided, I converted the chr2L.fa into chr2L.2bit using faToTwoBit

I got the same error using my own dataset.

Thank you

[tianxiongbb]

Hi,
Can you paste the command you used for running TEMP2 Absence?

[tianxiongbb]

I updated README to include the command for testing the absence module.
I also fixed a bug introduced in v1.0.2, when bwa-mem XS tag is used for inferring uniquely mapped reads. Can you re-download TEMP2 and see if it works?

[JBerthelier]

Dear Tianxong,

Thanks for your quick reply and help. I tried with your updated script and data, and the absent module is now working properly with the test data !

However, I have now issue with my own dataset, and I suspect the cause is my version of : FaToTwoBit, which seems not compatible.

I got this error message :

Can't open leaf_f1.fq.gz.excision.cluster.rpmk.refined.bp.sfcp since No such file or directory
[main_samview] region "Chr:1-505" specifies an invalid region or unknown reference. Continue anyway.
[main_samview] region "Chr:1-503" specifies an invalid region or unknown reference. Continue anyway.
Illegal division by zero at /home2020/home/uha/jberthel/Tools/TEMP/TEMP2/bin/summarize_excision.pl line 45, line 1.
(

Actually, I have the same error message when I use my own "chr2L.2bit" (from chr2L.fa test data) that I generated with with my version of FaToTwoBit. While I got no error with the "chr2L.2bit" your just shared.

Could you add your executable of FaToTwoBit in the /bin or maybe let me know which version I have to use ?

Thanks for your support,

[JBerthelier]

Hello,
I come back to you cause I am still stuck with this issue.
Would you have any suggestion(s) to help me ?

Thank you,

Best regards,

[tianxiongbb]

I added faToTwoBit to /bin. Can you please try to make the 2bit file using this script and let me know if it works?
faToTwoBit provided 32-bit and 64-bit offsets; the later is for large genome (>4Gb) and is probably not compatible with the TEMP2 absence mode.

Best,
Tianxiong