An Error in Step3 # splitting loci so first file is smaller and last file is bigger

[jljy47]

Hi, we met an Error in Step3 showing that

Message: KeyboardInterrupt: -> 1255 inclusts = iter(clustio.read().strip().split("//\n//\n")) 1257 # splitting loci so first file is smaller and last file is bigger

1) We're curious to know the cause and if it has anything to do with the original documents. Can we continue with it or have to restart it from Step3? 2) Is the Error caused by running with another ipyrad process in Step7 at the same time?( Message: KeyboardInterrupt: ) I did this once before but didn't have this problem.

The original code and message:

data.run("123456") Parallel` connection | nku-PowerEdge-T640: 60 cores [####################] 100% 0:05:36 | loading reads | s1 | [####################] 100% 0:50:53 | processing reads | s2 | [####################] 100% 0:43:29 | join merged pairs | s3 | [####################] 100% 1:12:11 | join unmerged pairs | s3 | [####################] 100% 0:40:03 | dereplicating | s3 | [####################] 100% 5 days, 3:47:53 | clustering/mapping | s3 || [####################] 100% 0:01:11 | building clusters | s3 | [####################] 100% 0:00:12 | chunking clusters | s3 |

Encountered an Error. Message: KeyboardInterrupt:

KeyboardInterrupt Traceback (most recent call last)

in ~/miniconda3/envs/ipyrad/lib/python3.9/site-packages/ipyrad/assemble/clustmap.py in muscle_chunker(data, sample) 1253 # write optim clusters to each tmp file 1254 clustio = open(clustfile, 'rt') -> 1255 inclusts = iter(clustio.read().strip().split("//\n//\n")) 1256 1257 # splitting loci so first file is smaller and last file is bigger KeyboardInterrupt: **data.run("4")** Parallel connection | nku-PowerEdge-T640: 60 cores skipping samples not in state==3: ['OUT1', 'OUT2', 'OUT3', 'cr-CQJFS1', 'cr-CQJFS2', 'cr-CQJFS3', 'cr-CQSZ1', 'cr-CQSZ2', 'cr-CQSZ3', 'cr-CQSZ4', 'cr-FJLY1', 'cr-GDCBL1', 'cr-GDNL1', 'cr-GDNL2', 'cr-GXCZ1', 'cr-GXCZ2', 'cr-GXGL1', 'cr-GXGL2', 'cr-GXHC1', 'cr-GXJX1', 'cr-GXJX2', 'cr-GZBJ1', 'cr-GZBJ2', 'cr-GZKKS1', 'cr-GZKKS2', 'cr-GZLD1', 'cr-GZLGS1', 'cr-GZLGS2', 'cr-GZLGS3', 'cr-GZLGS4', 'cr-GZLGS5', 'cr-HNNS1', 'cr-JXJGS1', 'cr-JXJGS2', 'cr-JXJGS3', 'cr-JXJGS4', 'cr-JXJLS1', 'cr-LAOS1', 'cr-SCDB1', 'cr-SCDB2', 'cr-SCDB3', 'cr-SCDB4', 'cr-SCDB5', 'cr-SCDB6', 'cr-SCDJY1', 'cr-SCDJY2', 'cr-SCDJY3', 'cr-SCDJY4', 'cr-SCDJY5', 'cr-SCLD1', 'cr-SCLD2', 'cr-SCLD3', 'cr-SCLD4', 'cr-SCLD5', 'cr-SCLD6', 'cr-SCLS1', 'cr-SCLS2', 'cr-SCLS3', 'cr-SCMY1', 'cr-SCMY2', 'cr-SCNC1', 'cr-SCNC2', 'cr-SCNC3', 'cr-SCQC1', 'cr-SCQC2', 'cr-SCWC1', 'cr-SNJE1', 'cr-SNJE2', 'cr-SNJY3', 'cr-SNJY5', 'cr-SXQL3', 'cr-SXQL4', 'cr-SXSY1', 'cr-SXSY2', 'cr-SXSY3', 'cr-SXSY4', 'cr-SXSY5', 'cr-SXYX1', 'cr-TWALS1', 'cr-TWALS2', 'cr-TWALS3', 'cr-TWGX1', 'cr-TWGX2', 'cr-TWGX3', 'cr-TWNT1', 'cr-TWNT2', 'cr-TWNTLS1', 'cr-TWNTLS2', 'cr-TWPD1', 'cr-TWTD1', 'cr-TWTS1', 'cr-TWTS2', 'cr-TWTS3', 'cr-TWXB1', 'cr-TWXB2', 'cr-TWYL1', 'cr-TWYL2', 'cr-XZBJL1', 'cr-XZBJL2', 'cr-XZBJL3', 'cr-XZBM1', 'cr-XZBM2', 'cr-XZBM3', 'cr-XZCY1', 'cr-XZCY2', 'cr-XZCY3', 'cr-XZCY4', 'cr-XZCY5', 'cr-XZJL1', 'cr-XZJL2', 'cr-XZJL3', 'cr-XZJL4', 'cr-XZSN1', 'cr-XZSN2', 'cr-YNDL1', 'cr-YNDL2', 'cr-YNDL3', 'cr-YNDL4', 'cr-YNDL5', 'cr-YNDQ1', 'cr-YNDQ2', 'cr-YNGN1', 'cr-YNGN2', 'cr-YNGN3', 'cr-YNGN4', 'cr-YNGN5', 'cr-YNHZ1', 'cr-YNHZ2', 'cr-YNHZ3', 'cr-YNHZ4', 'cr-YNHZ5', 'cr-YNHZ6', 'cr-YNJH1', 'cr-YNJH2', 'cr-YNJH3', 'cr-YNJH4', 'cr-YNJH5', 'cr-YNJP1', 'cr-YNJP2', 'cr-YNJP3', 'cr-YNKM2', 'cr-YNKM3', 'cr-YNKM4', 'cr-YNKM5', 'cr-YNLC1', 'cr-YNLC4', 'cr-YNLC5', 'cr-YNLS1', 'cr-YNLS2', 'cr-YNLS3', 'cr-YNLS4', 'cr-YNPB1', 'cr-YNPB2', 'cr-YNPB3', 'cr-YNRL1', 'cr-YNRL2', 'cr-YNRL3', 'cr-YNRL4', 'cr-YNSZ1', 'cr-YNSZ2', 'cr-YNSZ3', 'cr-YNSZ4', 'cr-YNSZ5', 'cr-YNYJ1', 'cr-YNYJ2', 'cr-YNYJ3', 'cr-YNYL1', 'cr-YNYL2', 'cr-YNYL3', 'cr-YNYL4', 'cr-YNYL5', 'cr-YNZT1', 'cr-ZJQY1', 'cr-ZJQY2', 'cr-ZJWYL1', 'cr_CRDPS1', 'cr_CRTC1', 'cr_CSXZY1', 'in-XZRKZ1', 'in-XZRKZ2', 'in-XZRKZ3', 'in-XZRKZ4', 'in-XZRKZ5'] Encountered an Error. Message: no samples ready for step 4 Traceback (most recent call last): File "/home/nku/miniconda3/envs/ipyrad/lib/python3.9/site-packages/ipyrad/core/Parallel.py", line 314, in wrap_run self.tool._run(ipyclient=self.ipyclient, **self.rkwargs) File "/home/nku/miniconda3/envs/ipyrad/lib/python3.9/site-packages/ipyrad/core/assembly.py", line 696, in _run stepdict[step](self, force, ipyclient).run() File "/home/nku/miniconda3/envs/ipyrad/lib/python3.9/site-packages/ipyrad/assemble/jointestimate.py", line 38, in __init__ self.samples = self.get_subsamples() File "/home/nku/miniconda3/envs/ipyrad/lib/python3.9/site-packages/ipyrad/assemble/jointestimate.py", line 89, in get_subsamples raise IPyradError("no samples ready for step 4") ipyrad.assemble.utils.IPyradError: no samples ready for step 4

Thank you so much~

[isaacovercast]

The KeyboardInterrupt error indicates that you either pushed ctrl+c or you pushed the stop button on the jupyter notebook. If you killed during step 3 then you will need to run step 3 over again. The reason it says 'no samples ready for step 4' when you try to run step 4 is because none of the samples finished running step 3. Please run step 3 again.

[jljy47]

So the error has nothing to do with this situation right？

1257 # splitting loci so first file is smaller and last file is bigger

[isaacovercast]

No, the error was not that, it was KeyboardInterrupt, which means the process was force quit. The line you indicate is a comment in the code on line 1257 to indicate what that code is doing and just happens to be where the code was executing when it was killed.

[jljy47]

Thank you so much for your help every time, Isaac~

[isaacovercast]

No prob!