the problem of output results

[snowylxx]

Hello. I use the MobiLLe to cluster BCRs. No errors were reported during operation. And the result files are all available. But each cluster has only one sequence. I think there must be a problem with this. So do you know the possible reason?

[julibinho]

Dear, To help you we need to take a look in your input file. best

[snowylxx]

Hello, julibinho. Thank you for your reply.

When I was debugging an error, I found that line 95 in the Mobile.sh code: OutPath=$OPTARG should be changed to OutputPath=$OPTARG. Otherwise, the parameter - o is actually useless.

I modified my input file according to the example provided, but some column information is still incomplete. I'm not sure if the error is due to formatting issues or missing information in certain columns.

the error: Traceback (most recent call last): File "/storage/work/lixx/software/MobiLLe/Code/src/Cluster_distribution_plot.py", line 180, in main() File "/storage/work/lixx/software/MobiLLe/Code/src/Cluster_distribution_plot.py", line 175, in main Plot(Dicoresult,Dataset_name,adress_tempo_file,uniformity_data) File "/storage/work/lixx/software/MobiLLe/Code/src/Cluster_distribution_plot.py", line 100, in Plot plt.xlim(xmax = abundance[-1]+abundance[-1]/3, xmin = -(abundance[-1]/10)) IndexError: list index out of range

So Can you give me your email address so that I can send you the input file.

[julibinho]

Thanks for this feedback, you can send your input to @.***

Best regards

Le mer. 27 sept. 2023 à 11:19, snowylxx @.***> a écrit :

Hello, julibinho. Thank you for your reply.

When I was debugging an error, I found that line 95 in the Mobile.sh code: OutPath=$OPTARG should be changed to OutputPath=$OPTARG. Otherwise, the parameter - o is actually useless.

I modified my input file according to the example provided, but some column information is still incomplete. I'm not sure if the error is due to formatting issues or missing information in certain columns.

the error: Traceback (most recent call last): File "/storage/work/lixx/software/MobiLLe/Code/src/Cluster_distribution_plot.py", line 180, in main() File "/storage/work/lixx/software/MobiLLe/Code/src/Cluster_distribution_plot.py", line 175, in main Plot(Dicoresult,Dataset_name,adress_tempo_file,uniformity_data) File "/storage/work/lixx/software/MobiLLe/Code/src/Cluster_distribution_plot.py", line 100, in Plot plt.xlim(xmax = abundance[-1]+abundance[-1]/3, xmin = -(abundance[-1]/10)) IndexError: list index out of range

So Can you give me your email address so that I can send you the input file.

— Reply to this email directly, view it on GitHub https://github.com/julibinho/MobiLLe/issues/4#issuecomment-1737025905, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACMJX7DEUFZD73TMZ2T4L7TX4PVSHANCNFSM6AAAAAA45X257U . You are receiving this because you commented.Message ID: @.***>

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Juliana Silva Bernardes, Assistant Professor. Biologie Computationnelle et Quantitative Sorbonne Université, Paris, France http://www.lcqb.upmc.fr/julianab 01 44 27 91 61

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[snowylxx]

I can't see the email adress. Maybe it's because Github restricted it.

you can see the input file in the link below： https://workdrive.zoho.com.cn/file/jy0759bda1394301c4799897844b151d9f95e

[julibinho]

ok, I got it, I will check and let you know. best

Le mer. 27 sept. 2023 à 11:39, snowylxx @.***> a écrit :

I can't see the email adress. Maybe it's because Github restricted it.

you can see the input file in the link below： https://workdrive.zoho.com.cn/file/jy0759bda1394301c4799897844b151d9f95e

— Reply to this email directly, view it on GitHub https://github.com/julibinho/MobiLLe/issues/4#issuecomment-1737057069, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACMJX7A45CXZKE6K6HDVKTDX4PX5HANCNFSM6AAAAAA45X257U . You are receiving this because you commented.Message ID: @.***>

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Juliana Silva Bernardes, Assistant Professor. Biologie Computationnelle et Quantitative Sorbonne Université, Paris, France http://www.lcqb.upmc.fr/julianab 01 44 27 91 61

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[snowylxx]

you are so nice. Thank you and look forward to your reply.

Best wishes

[julibinho]

Dear user,

I tried your input file and it seems to work fine. Find here the outputs: https://www.lcqb.upmc.fr/julianab/HDR/Test.zip I created a folder Test into Input, and I put your file inside. I also created a folder into Output named Test, I created a parameter file named pars.txt = https://www.lcqb.upmc.fr/julianab/HDR/pars.txt

Then I called MobiLLe in the terminal with:

bash Mobille.sh -f pars.txt

Let me know if you can reproduce it.

best

Find below the log for this execution. ##########################################################

Mobille

########################################################## Clustering begins... Output/Test/toy_dataset_seq_Fo.txt end of clustering

Refinement begins...

/home/julianab/anaconda3/lib/python3.7/site-packages/Bio/SubsMat/init.py:131: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module. BiopythonDeprecationWarning, end of refinement

Formating the output files...

/home/julianab/anaconda3/lib/python3.7/site-packages/Bio/SubsMat/init.py:131: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module. BiopythonDeprecationWarning, The results are ready to explore here : Output/Test/

Le mer. 27 sept. 2023 à 11:46, snowylxx @.***> a écrit :

you are so nice. Thank you and look forward to your reply.

Best wishes

— Reply to this email directly, view it on GitHub https://github.com/julibinho/MobiLLe/issues/4#issuecomment-1737067557, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACMJX7F3NFNIOAWJVLRIJ63X4PYWFANCNFSM6AAAAAA45X257U . You are receiving this because you commented.Message ID: @.***>

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Juliana Silva Bernardes, Assistant Professor. Biologie Computationnelle et Quantitative Sorbonne Université, Paris, France http://www.lcqb.upmc.fr/julianab 01 44 27 91 61

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[snowylxx]

Dear author；

I previously operated the data on the RStudio server for the convenience of other data analysis previous. After reading your reply, I used another termination tool and ran the program again, and it worked!!
Of course, errors may still be reported on the RStudio server, which may be related to some related configurations. But the specific reason is unknown.

There are actually many NA columns in my file. I would like to ask if I can skip those NA columns, as they were all added later by me. What are the necessary columns and are there any requirements for the column order?

[julibinho]

Dear user,

Mobille needs the following columns: productive position 5 V gene position 10 J gene position 12 CDR3 position 29 Vseq position 86 Vseq_aa position 87 Jseq position 90 Jseq_aa position 91

I recommend keeping NA since the script considers de positions in the file.

Best regards, Juliana

Le jeu. 28 sept. 2023 à 04:37, snowylxx @.***> a écrit :

Dear author；

I previously operated the data on the RStudio server for the convenience of other data analysis previous. After reading your reply, I used another termination tool and ran the program again, and it worked!! Of course, errors may still be reported on the RStudio server, which may be related to some related configurations. But the specific reason is unknown.

There are actually many NA columns in my file. I would like to ask if I can skip those NA columns, as they were all added later by me. What are the necessary columns and are there any requirements for the column order?

— Reply to this email directly, view it on GitHub https://github.com/julibinho/MobiLLe/issues/4#issuecomment-1738354489, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACMJX7FIPPLOTHQHEKC4GGTX4TPGTANCNFSM6AAAAAA45X257U . You are receiving this because you commented.Message ID: @.***>

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Juliana Silva Bernardes, Assistant Professor. Biologie Computationnelle et Quantitative Sorbonne Université, Paris, France http://www.lcqb.upmc.fr/julianab 01 44 27 91 61

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[snowylxx]

Dear author: thanks for your reply. here I have another question. There are over 4 million lines of bcr data in my input file. Is there any way to make the program run faster？ or multithreaded?