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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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Alpha_rarefraction.py error #2217

Open santhoshnh opened 5 years ago

santhoshnh commented 5 years ago

Hello, I am running alph_rarefraction.py for one of my sample. But i am getting an error. The Matrices generations running successfully. But after that, alpha diveristy plots are not creating. it gives the below error

Traceback (most recent call last): File "/home/bgc/.conda/envs/qiime1/bin/alpha_rarefaction.py", line 4, in import('pkg_resources').run_script('qiime==1.9.1', 'alpha_rarefaction.py') File "/home/bgc/.conda/envs/qiime1/lib/python2.7/site-packages/pkg_resources/init.py", line 750, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/bgc/.conda/envs/qiime1/lib/python2.7/site-packages/pkg_resources/init.py", line 1527, in run_script exec(code, namespace, namespace) File "/home/bgc/.conda/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/alpha_rarefaction.py", line 161, in main() File "/home/bgc/.conda/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/alpha_rarefaction.py", line 158, in main retain_intermediate_files=retain_intermediate_files) File "/home/bgc/.conda/envs/qiime1/lib/python2.7/site-packages/qiime/workflow/downstream.py", line 342, in run_alpha_rarefaction close_logger_on_success=close_logger_on_success) File "/home/bgc/.conda/envs/qiime1/lib/python2.7/site-packages/qiime/workflow/util.py", line 122, in call_commands_serially raise WorkflowError(msg) qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: Rarefaction plot: All metrics Command run was: make_rarefaction_plots.py -i arare/alpha_div_collated/ -m mappingfile.csv_corrected.txt -o arare/alpha_rarefaction_plots/ --background_color white --resolution 80 --imagetype png Command returned exit status: 1 Stdout:

Stderr Traceback (most recent call last): File "/home/bgc/.conda/envs/qiime1/bin/make_rarefaction_plots.py", line 4, in import('pkg_resources').run_script('qiime==1.9.1', 'make_rarefaction_plots.py') File "/home/bgc/.conda/envs/qiime1/lib/python2.7/site-packages/pkg_resources/init.py", line 750, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/bgc/.conda/envs/qiime1/lib/python2.7/site-packages/pkg_resources/init.py", line 1527, in run_script exec(code, namespace, namespace) File "/home/bgc/.conda/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/make_rarefaction_plots.py", line 229, in main() File "/home/bgc/.conda/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/make_rarefaction_plots.py", line 219, in main generate_average_tables=generate_average_tables) File "/home/bgc/.conda/envs/qiime1/lib/python2.7/site-packages/qiime/make_rarefaction_plots.py", line 578, in make_averages new_ymax = (max([max(v) for v in rares_data['series'].values()]) + ValueError: max() arg is an empty sequence

Because of this error I stuck with my analysis. It will be more helpful for me, if you help me to solve this issue.

Thank you

Samia741 commented 5 years ago

hello everyone, I am Samia. I am using QIIME1 and did all following steps before the alpha diversity. But getting one error in the following stepalpha_rarefaction.py -i otus/otu_table.biom -m map_fluid_1.txt -o alpha_fluid_1 -p alpha_params.txt -t otus/rep_set.tre My purpose is to get the OTU_table_Description.txt, sees_rep_set.fasta, taxa summary and PCoA. I have tried many ways but cannot solve this problem in this step. Please, help me.