Error while running align_get_align_summary_data

[bheimbu]

Hi, I am experiencing following error while running align_get_align_summary_data:

$ phyluce_align_get_align_summary_data --alignments mafft/ --cores 20 --log-path log/ 2020-07-06 09:30:42,229 - phyluce_align_get_align_summary_data - INFO - ========= Starting phyluce_align_get_align_summary_data ========= 2020-07-06 09:30:42,230 - phyluce_align_get_align_summary_data - INFO - Version: 1.5.0 2020-07-06 09:30:42,230 - phyluce_align_get_align_summary_data - INFO - Argument --alignments: /home/uni08/bheimbu/bin/Paper_2/UCE/phyluce/master_list_subset_amitermes/taxon_sets/all/mafft 2020-07-06 09:30:42,230 - phyluce_align_get_align_summary_data - INFO - Argument --cores: 20 2020-07-06 09:30:42,230 - phyluce_align_get_align_summary_data - INFO - Argument --input_format: nexus 2020-07-06 09:30:42,230 - phyluce_align_get_align_summary_data - INFO - Argument --log_path: /home/uni08/bheimbu/bin/Paper_2/UCE/phyluce/master_list_subset_amitermes/taxon_sets/all/log 2020-07-06 09:30:42,230 - phyluce_align_get_align_summary_data - INFO - Argument --show_taxon_counts: False 2020-07-06 09:30:42,230 - phyluce_align_get_align_summary_data - INFO - Argument --verbosity: INFO 2020-07-06 09:30:42,230 - phyluce_align_get_align_summary_data - INFO - Getting alignment files 2020-07-06 09:30:42,241 - phyluce_align_get_align_summary_data - INFO - Computing summary statistics using 20 cores /usr/users/bheimbu/.conda/envs/phyluce/lib/python2.7/site-packages/numpy/core/_methods.py:55: RuntimeWarning: Mean of empty slice. warnings.warn("Mean of empty slice.", RuntimeWarning) /usr/users/bheimbu/.conda/envs/phyluce/lib/python2.7/site-packages/numpy/core/_methods.py:67: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) /usr/users/bheimbu/.conda/envs/phyluce/lib/python2.7/site-packages/numpy/core/_methods.py:79: RuntimeWarning: Degrees of freedom <= 0 for slice warnings.warn("Degrees of freedom <= 0 for slice", RuntimeWarning) /usr/users/bheimbu/.conda/envs/phyluce/lib/python2.7/site-packages/numpy/core/_methods.py:91: RuntimeWarning: invalid value encountered in true_divide arrmean, rcount, out=arrmean, casting='unsafe', subok=False) /usr/users/bheimbu/.conda/envs/phyluce/lib/python2.7/site-packages/numpy/core/_methods.py:113: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) Traceback (most recent call last): File "/usr/users/bheimbu/.conda/envs/phyluce/bin/phyluce_align_get_align_summary_data", line 292, in <module> main() File "/usr/users/bheimbu/.conda/envs/phyluce/bin/phyluce_align_get_align_summary_data", line 267, in main a_vars = get_lengths(summary) File "/usr/users/bheimbu/.conda/envs/phyluce/bin/phyluce_align_get_align_summary_data", line 120, in get_lengths min = numpy.min(lengths) File "/usr/users/bheimbu/.conda/envs/phyluce/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2214, in amin out=out, keepdims=keepdims) File "/usr/users/bheimbu/.conda/envs/phyluce/lib/python2.7/site-packages/numpy/core/_methods.py", line 21, in _amin out=out, keepdims=keepdims) ValueError: zero-size array to reduction operation minimum which has no identity

I have checked my folder mafft and it includes fasta files. Do you know what's wrong here?

Cheers Bastian

[Lostinthecodingsauce]

I am also getting this error. I have gotten it both within the tutorial and with my own data.

[brantfaircloth]

Have you both checked to ensure that you don't have a file with either an empty or a very short alignment? Additionally, I can't do much to help without some example data...

[Lostinthecodingsauce]

Hello Brant,

Here is my alignment data. Please let me know if there is anything else that I should send you.

Best, Ben Pir-alignment.zip https://drive.google.com/file/d/16jTs0LI3Ag86zzM6p-a2Ps9yF_wm9XTJ/view?usp=drive_web

On Fri, Jul 17, 2020 at 11:35 AM Brant Faircloth notifications@github.com wrote:

Have you both checked to ensure that you don't have a file with either an empty or a very short alignment? Additionally, I can't do much to help without some example data...

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/faircloth-lab/phyluce/issues/196#issuecomment-660274373, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALOMO2PEYOM2HTVKWDQKRCTR4CKVPANCNFSM4ORKOULA .

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Benjamin Scott Graduate Student/Teaching Assistant M.S. Evolutionary Biology student San Diego State University

[brantfaircloth]

Google Drive suggests that I don't have access to those files... I sent a request w/ my google username.

[brantfaircloth]

The format of your output files appears to be 'fasta' and not 'nexus'. The default that is expected is 'nexus'. It should work if you run:

phyluce_align_get_align_summary_data --alignments mafft-nexus --input-format fasta --cores 4

[Lostinthecodingsauce]

I cannot believe I did not catch that. Thank you for your help on such a minor issue. Perhaps the stir-craziness is turning into actual craziness now.. Thanks again!

On Fri, Jul 17, 2020 at 12:15 PM Brant Faircloth notifications@github.com wrote:

The format of your output files appears to be 'fasta' and not 'nexus'. The default that is expected is 'nexus'. It should work if you run:

phyluce_align_get_align_summary_data --alignments mafft-nexus --input-format fasta --cores 4

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/faircloth-lab/phyluce/issues/196#issuecomment-660292625, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALOMO2MQWED6KKUWL464TWTR4CPOPANCNFSM4ORKOULA .

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Benjamin Scott Graduate Student/Teaching Assistant M.S. Evolutionary Biology student San Diego State University