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degregory / SAM_Refiner

Program for gathering variant information from a SAM formated file.
GNU General Public License v3.0
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Processing errors #1

Closed EvolDoc closed 3 years ago

EvolDoc commented 3 years ago

Greetings, I have encountered errors at the end of each of my analyses. Any suggestions?

Starting SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 processing At read 5000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 5000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 10000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 10000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 15000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 15000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 20000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 20000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 25000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 25000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 30000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 30000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 35000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 35000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 40000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 40000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 45000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 45000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 50000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 50000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 55000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 55000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 60000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 60000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 65000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 65000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 70000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 70000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 75000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 75000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 80000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 80000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 85000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 85000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 90000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 90000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM At read 95000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 At line 95000 of SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 SAM End SAM parse for SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 End unqiue seq out for SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 End indel out for SARSCT-WastewaterxxSechristxxSWIFTxxNAUxx20210414-xx-xx-xxx-xxxx-169-CH_S50 Process Process-4: Traceback (most recent call last): File "/packages/anaconda3/2020.11/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/packages/anaconda3/2020.11/lib/python3.8/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/scratch/cmh574/software/Sam_Refiner.py", line 820, in SAMparse AAinfo = singletCodon(POS, ref[1][POS-1], ref) File "/scratch/cmh574/software/Sam_Refiner.py", line 408, in singletCodon codon = nt+ref[1][ntPOS]+ref[1][ntPOS+1] IndexError: string index out of range

degregory commented 3 years ago

I've put in what might be a quick fix if you want to try again. If it doesn't work, if you'd be willing to share the reference and one of the sam files you are using I'll work on troubleshooting.

EvolDoc commented 3 years ago

Definitely :-) I'll try right now.

EvolDoc commented 3 years ago

Its working!! Thanks so much!