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Hi @isaacovercast I am new to programming, ipyrad and to computing on the cluster. I have run ipyrad successfully on my local machine, and also on my institution's cluster, but I am running into issues running ipyrad on multiple nodes. On the help documentation, it is suggested to use "module load MPI". My institution has a ton of MPI modules, and I am not sure which one is appropriate. Are you able to help me out? Does the --MPI tag still work with these? Anything else special I need to do? @^~^@ module avail openmpi
------------------------------ /etc/modulefiles -------------------------------
openmpi-1.4-psm-x86_64 openmpi-1.5.3-psm-x86_64
openmpi-1.4-x86_64 openmpi-1.5.3-x86_64
------------------------------ /act/modulefiles -------------------------------
openmpi-1.10.0-intel openmpi-1.8-intel
openmpi-1.6/gcc openmpi-1.8-intel-14.0.4
openmpi-1.6/gcc-4.7.2 openmpi-1.8-psm/gcc
openmpi-1.6/lua-5.3.0 openmpi-1.8-psm/gcc-4.7.2
openmpi-1.6-psm/gcc openmpi-2.0.0-intel-15.0.1
openmpi-1.6-psm/gcc-4.7.2 openmpi-2.0.0-intel-16.0.3
openmpi-1.8/gcc openmpi-2.1.0-intel-17.0.2
openmpi-1.8/gcc-4.7.2 openmpi-2.1.3-intel-17.0.6
[Tue Dec 29 09:58:21] xhuang@login01
~
@^~^@ module avail mvapich
------------------------------ /act/modulefiles -------------------------------
mvapich/gcc mvapich2-2.0-psm/gcc-4.7.2
mvapich/gcc-4.7.2 mvapich2-2.1-intel-14.0.4
mvapich2-2.0/gcc mvapich2-2.1-intel-15.0.1
mvapich2-2.0/gcc-4.7.2 mvapich2-2.2-psm
mvapich2-2.0-psm/gcc
I could get the error, why I got it, what is source of the problem, Dear Issac could you please suggest me what I did wrong.
IndexError: list index out of range
$ ipyrad -p params-parus_whole.txt -s 1
Traceback (most recent call last):
File "/anaconda3/bin/ipyrad", line 10, in <module>
sys.exit(main())
File "/anaconda3/lib/python3.7/site-packages/ipyrad/main.py", line 598, in main
CLI()
File "/anaconda3/lib/python3.7/site-packages/ipyrad/main.py", line 69, in init
self.get_assembly()
File "/anaconda3/lib/python3.7/site-packages/ipyrad/main.py", line 369, in get_assembly
data.set_params(key, param)
File "/anaconda3/lib/python3.7/site-packages/ipyrad/core/assembly.py", line 492, in set_params
setattr(self.params, param, newvalue)
File "/anaconda3/lib/python3.7/site-packages/ipyrad/core/params.py", line 730, in pop_assign_file
self._data._link_populations()
File "/anaconda3/lib/python3.7/site-packages/ipyrad/core/assembly.py", line 401, in _link_populations
for i in minlist})
File "/anaconda3/lib/python3.7/site-packages/ipyrad/core/assembly.py", line 401, in <dictcomp>
for i in minlist})
IndexError: list index out of range
Hi @isaacovercast thank you for your help earlier. I got everything up and running smoothly. I have been trying to troubleshoot an issue for the last couple of days, and have had no luck finding answers elsewhere. I am hoping you might know what to do, or at least point me in the right direction.
I am running STRUCTURE using these instructions here: https://ipyrad.readthedocs.io/en/latest/API-analysis/cookbook-structure.html# and I am running Jupyter notebook on my institutions HPC cluster using these instructions: https://github.com/dereneaton/ipyrad/blob/master/docs/HPC_Tunnel.rst
I have Jupyter notebook up and running and I can get steps/boxes 1-8 of the STRUCTURE cookbook to seemingly run without errors, but when I try to run box 9 (creating an etable under the header Analyze results: Choosing K), I get the following error: "IndexError: list index out of range".
This does not happen when I run the same exact thing on my local machine. Any thoughts here?
@isaacovercast Hi, Issac!
I finished running Rad-seq assembly for pair-end data and successfully gained output. But I only got .loci .phy .nex and so on.
However for my downstream analysis(searching for SSR and design primer out of it) I will need .fasta.
Do you have any idea how can I convert any of them to .fasta for next step?
Sorry I don't know whether it's ok to ask you about this here. I would really appreciate your help!
Step 3: Clustering/Mapping reads within samples
skipping samples not yet in state==2:
['CAYU_15A']
[####################] 100% 0:03:13 | join merged pairs
[####################] 100% 0:02:46 | join unmerged pairs
[####################] 100% 0:02:47 | dereplicating
[################## ] 92% 2 days, 22:11:29 | clustering/mapping
Please check with other users in your lab or the author to see if this is expected.
[andreeab@gra490 ~]$ top
top - 09:25:09 up 8 days, 18:22, 1 user, load average: 3.06, 3.05, 3.07
Tasks: 579 total, 1 running, 578 sleeping, 0 stopped, 0 zombie
%Cpu(s): 12.1 us, 0.1 sy, 0.0 ni, 87.8 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
KiB Mem : 13162476+total, 97422176 free, 27608988 used, 6593596 buff/cache
KiB Swap: 10485756 total, 10485756 free, 0 used. 99957064 avail Mem
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ P COMMAND
7761 andreeab 20 0 9902.0m 4.662g 356 S 132.1 3.7 5533:59 14 vsearch
7755 andreeab 20 0 18.576g 7.805g 352 S 128.9 6.2 5286:43 2 vsearch
7762 andreeab 20 0 6107388 3.588g 356 S 125.2 2.9 5047:53 12 vsearch
24752 andreeab 20 0 139464 2256 1248 R 1.6 0.0 0:00.50 20 top
4446 andreeab 20 0 739740 166384 15080 S 0.3 0.1 22:37.56 22 ipyrad
4465 andreeab 20 0 100128 37240 724 S 0.3 0.0 6:41.43 24 ipcluster
4467 andreeab 20 0 458528 147332 3940 S 0.3 0.1 12:10.94 26 python3.7
4512 andreeab 20 0 992392 194532 13864 S 0.3 0.1 1:20.33 26 python3.7
[andreeab@gra553 ~]$ top -u $USER
top - 09:34:46 up 8 days, 18:31, 1 user, load average: 3.17, 3.24, 3.26
Tasks: 558 total, 1 running, 557 sleeping, 0 stopped, 0 zombie
%Cpu(s): 46.6 us, 1.4 sy, 0.0 ni, 52.0 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
KiB Mem : 13162476+total, 94148064 free, 31876356 used, 5600340 buff/cache
KiB Swap: 10485756 total, 10311164 free, 174592 used. 95985096 avail Mem
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ P COMMAND
24937 andreeab 20 0 28.107g 0.013t 352 S 195.0 10.4 5406:59 8 vsearch
24939 andreeab 20 0 10.774g 4.575g 352 S 100.0 3.6 5519:20 7 vsearch
24940 andreeab 20 0 7635928 3.966g 352 S 95.0 3.2 5532:40 5 vsearch
10962 andreeab 20 0 139464 2004 1224 R 20.0 0.0 0:00.08 11 top
10903 andreeab 20 0 183424 2832 1008 S 0.0 0.0 0:00.00 10 sshd
10904 andreeab 20 0 126208 2548 1700 S 0.0 0.0 0:00.04 18 bash
17477 andreeab 20 0 462724 13288 7988 S 0.0 0.0 0:03.10 19 orted
17486 andreeab 20 0 988948 190212 13764 S 0.0 0.1 1:13.78 2 python3.7
17487 andreeab 20 0 1185856 389832 13776 S 0.0 0.3 1:14.17 31 python3.7
17488 andreeab 20 0 940776 140960 13088 S 0.0 0.1 0:38.71 9 python3.7
17489 andreeab 20 0 1028408 229460 13708 S 0.0 0.2 1:10.15 19 python3.7
17490 andreeab 20 0 978328 179192 13532 S 0.0 0.1 1:04.10 19 python3.7
@QiuyuJiang_twitter It's totally ok to ask about this here! The .phy output file is probably closest to a concatenated fasta format, but you'll have to do a little work to reformat it. Shouldn't be too hard. Good luck!
Thank you for your help! I am going to look up to it.