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zachary-foster / alignreads

A wrapper for YASRA and associated parsing scripts
GNU General Public License v2.0
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list index out of range #11

Open jkleinkopf opened 7 years ago

jkleinkopf commented 7 years ago

Hi Zachary,

I have been trying to figure out alignreads (and YASRA) to map reads to a reference made up of probe sequences. We want to keep the "splash zones" for our phylogenetic analyses, but have had trouble doing so in BWA. However, we keep getting errors with this program - first was the single-step error which we figured out quickly, but now we are getting the error

Traceback (most recent call last): File "/home/wade/Documents/alignreads/alignreads.py", line 467, in reload(makeconsensus) File "/home/wade/Documents/alignreads/makeconsensus.py", line 207, in pileups = list(readtools.PileupIO.parse(samPath, 'sam', applyPadding = False)) File "/home/wade/Documents/alignreads/readtools.py", line 994, in parse for pileup in formatParsers[fileFormat](handleOrPath, applyPadding): File "/home/wade/Documents/alignreads/readtools.py", line 944, in readSam yield Pileup(alignments = pileupAlignments, padAlignments = applyPadding, name = pileupAlignments[0].reference) IndexError: list index out of range

Here is the run-time info from that run:

=== Run-time information === [2017-09-11 13:45:51,930] DEBUG alignreads 305 Validating input arguments... [2017-09-11 13:45:51,930] DEBUG alignreads 320 Validating input arguments complete. [2017-09-11 13:45:52,008] DEBUG alignreads 337 Checking for YASRA... [2017-09-11 13:45:52,029] DEBUG alignreads 352 YASRA executable found at /home/wade/Documents/alignreads/bin. [2017-09-11 13:45:52,030] DEBUG alignreads 356 Checking for lastz... [2017-09-11 13:45:52,036] DEBUG alignreads 370 Version 1.03.02 of LASTZ found at /home/wade/Documents/alignreads/bin/lastz. [2017-09-11 13:45:52,036] DEBUG alignreads 374 Checking for nucmer... [2017-09-11 13:45:52,091] DEBUG alignreads 382 Version 3.1 of LASTZ found at /home/wade/Documents/alignreads/bin/nucmer. [2017-09-11 13:45:52,091] DEBUG alignreads 388 Executing runyasra... [2017-09-11 13:45:52,091] INFO alignreads 393 Implimenting YASRA with runyasra.py using the following command line: runyasra.py --percent-identity medium --lastz-binary-path /home/wade/Documents/alignreads/bin/lastz --yasra-binary-path /home/wade/Documents/alignreads/bin --read-type solexa --orientation linear --single-step --output-directory /media/wade/Files/Joseph/alignreadsPractice /media/wade/Files/Joseph/alignreadsPractice/CaffW_cleaned_concat.fa /media/wade/Files/Joseph/alignreadsPractice/blocks_for_probe_design_SINGLEREF.fasta [2017-09-11 13:45:52,563] DEBUG runyasra 139 Creating the YASRA makefile... [2017-09-11 13:45:52,563] DEBUG runyasra 325 YASRA makefile created. [2017-09-11 13:45:59,080] DEBUG alignreads 409 Execution of runyasra complete... [2017-09-11 13:45:59,081] DEBUG alignreads 431 Preparing output folder for post-yasra anaylsis.... [2017-09-11 13:45:59,082] DEBUG alignreads 453 Prepartion of output folder for post-yasra anaylsis complete. [2017-09-11 13:45:59,082] DEBUG alignreads 457 Executing makeconsensus... [2017-09-11 13:45:59,085] CRITICAL alignreads 469 An error occured during execution of makeconsensus.py: [2017-09-11 13:45:59,085] DEBUG alignreads 477 Execution of makeconsensus complete.

We are having a bit of trouble figuring out where the program is having problems, but maybe something in YASRA is not working for us?

Thanks, Joseph

zachary-foster commented 7 years ago

Sorry for the trouble @jkleinkopf! I will look into it and get back to you