Empty output after running examples

[mauriciomr1985]

Hi,

I'm trying to run one of your examples, but the results.txt is always empty.

This is the command line I used: differentialBindingAffinity_multipleSNPs examples/combined_Jaspar2022_Hocomoco_Kellis_human_transfac.txt examples/SNPs_EFO_0000612_myocardial_infarction.bed reference_genome_hg38/reference_genome_hg38.fa

This is the output (apparently, no errors): HELLO PFM dir: examples/combined_Jaspar2022_Hocomoco_Kellis_human_transfac.txt SNP file: examples/SNPs_EFO_0000612_myocardial_infarction.bed genome file: reference_genome_hg38/reference_genome_hg38.fa index file reference_genome_hg38/reference_genome_hg38.fa.fai not found, generating... number SNPs: 1665 numMotifs: 817 number of tests: 1360305 rank bevor correction: 968353 rank after correction: 0

The reference genome I downloaded from here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ (hg38.chromFa.tar.gz file). After I download, I concatenate all chromosomes in a single .fa file. I included first chr1 to chrY, and then the rest in a sorted order (show part of the file below): 1:>chr1 4979131:>chr2 9823003:>chr3 13788916:>chr4 17593209:>chr5 21223976:>chr6 24640097:>chr7 27827018:>chr8 30729792:>chr9 33497688:>chr10 36173638:>chr11 38875372:>chr12 41540880:>chr13 43828168:>chr14 45969044:>chr15 48008869:>chr16 49815637:>chr17 51480787:>chr18 53088254:>chr19 54260608:>chr20 55549493:>chr21 56483694:>chr22 57500065:>chrX 60620884:>chrY 61765434:>chr10_GL383545v1_alt 61769021:>chr10_GL383546v1_alt 61775219:>chr10_KI270824v1_alt 61778850:>chr10_KI270825v1_alt 61782618:>chr11_GL383547v1_alt 61785708:>chr11_JH159136v1_alt 61789729:>chr11_JH159137v1_alt 61793559:>chr11_KI270721v1_random (...)

I attached here some of the output files (I modified to .txt so github allows me to upload them)

result.txt motifInfo.txt notConsideredSNPs.txt TF_count.txt SNPsUnique.txt snpRegions.txt info.txt

I would appreciate your help on this matter. The program looks very good, by the way.

[biouserPD]

Hi, I also had the same problem. I used a genome from a non-model species (correctly renamed with chr1,chr2...)and a .bed file built following your instructions. The analysis seems to be successful without errors but the results.txt file only has the header and is empty. I'm agree that the program looks very good. Thanks for your help

[SchulzLab]

Hello, thank you for pointing out the problem, we will look into it.

Regards, Marcel

[BaumgartenNina]

Hi @biouserPD and @mauriciomr1985,

sorry for the late reply.

I was able to reproduce the error both of you got. The issue is that one needs to provide a scale file, which I added to the git hub repo (necessaryInputFiles/estimatedScalesPerMotif_1.9.txt). Otherwise sneep cannot compute a p-value for the differential TF binding score and will set it to 1, which result in an empty result file (since no sig. result is obtained).

If you run the following command, do you still observe a non-empty result file?

differentialBindingAffinity_multipleSNPs -s necessaryInputFiles/estimatedScalesPerMotif_1.9.txt examples/combined_Jaspar2022_Hocomoco_Kellis_human_transfac.txt examples/SNPs_EFO_0000612_myocardial_infarction.bed <path_to_hg38>

I am going to update the ReadTheDocs accordingly as soon as possible. (Also for Example 1 in ReadTheDocs a file is missing, so you might skip this for now.)

Sorry for the issue and thanks a lot for your feedback and especially for your patience!

Nina

[BaumgartenNina]

Hi again,

modified sneep in such a way that the scale file is a required input (no longer given with the flag -s) to avoid the here mentioned problem. The code on github is up-to-date. Based on our experience it usually takes a few days until the bioconda packages is updated as well. I also adapted ReadTheDocs accordingly. The command I gave in the previous comment, changes in the updated sneep version to:

differentialBindingAffinity_multipleSNPs examples/combined_Jaspar2022_Hocomoco_Kellis_human_transfac.txt examples/SNPs_EFO_0000612_myocardial_infarction.bed <path-to-genome-file> necessaryInputFiles/estimatedScalesPerMotif_1.9.txt

I hope the bioconda package is updated soon! Nina

[biouserPD]

Hi Nina, thanks so much for the quick response and the update. I tried to run the same analysis with my non-model species and now however I have a core dumped error. I'll try to investigate the problem better. I will soon try the example coming with Sneep software and I will keep you updated. Thanks again Max

Il giorno mer 13 dic 2023 alle ore 14:03 BaumgartenNina < @.***> ha scritto:

Hi again,

modified sneep in such a way that the scale file is a required input (no longer given with the flag -s) to avoid the here mentioned problem. The code on github is up-to-date. Based on our experience it usually takes a few days until the bioconda packages is updated as well. I also adapted ReadTheDocs accordingly. The command I gave in the previous comment, changes in the updated sneep version to:

differentialBindingAffinity_multipleSNPs examples/combined_Jaspar2022_Hocomoco_Kellis_human_transfac.txt examples/SNPs_EFO_0000612_myocardial_infarction.bed necessaryInputFiles/estimatedScalesPerMotif_1.9.txt

I hope the bioconda package is updated soon! Nina

— Reply to this email directly, view it on GitHub https://github.com/SchulzLab/SNEEP/issues/8#issuecomment-1853879406, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVMHEKTUZA5S6WMIM5Q6VTYJGRRHAVCNFSM6AAAAABABTCDF2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJTHA3TSNBQGY . You are receiving this because you were mentioned.Message ID: @.***>

-- Massimiliano Babbucci, PhD Department of Comparative Biomedicine and Food Science (BCA) University of Padova Viale dell'Universita' 16, Agripolis I-35020 Legnaro (PD), Italy ORCID: https://orcid.org/0000-0002-4060-4728 Tel: + 39 049 8272941 e-mail: @.***

[SchulzLab]

Hello, we were wondering if SNEEP now works for you with the updated bioconda package?

Kind regards, Marcel

[biouserPD]

Hello, the last time I used SNEEP was about two months ago and it still gave me an empty output file. In the next few days I will try again by installing the software via conda and I will let you know. Unfortunately I use a non model species for the analysis and I'm trying to figure out if there's a way to apply your software in the best way. I will keep you updated. Thanks a lot, Max

Il giorno lun 18 mar 2024 alle ore 14:17 SchulzLab @.***> ha scritto:

Hello, we were wondering if SNEEP now works for you with the updated bioconda package?

Kind regards, Marcel

— Reply to this email directly, view it on GitHub https://github.com/SchulzLab/SNEEP/issues/8#issuecomment-2003881302, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVMHEKOV4IXG7EM5ED7Z5DYY3SM5AVCNFSM6AAAAABABTCDF2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBTHA4DCMZQGI . You are receiving this because you were mentioned.Message ID: @.***>

-- Massimiliano Babbucci, PhD Department of Comparative Biomedicine and Food Science (BCA) University of Padova Viale dell'Universita' 16, Agripolis I-35020 Legnaro (PD), Italy ORCID: https://orcid.org/0000-0002-4060-4728 Tel: + 39 049 8272506 e-mail: @.***

[biouserPD]

Hello, I used the conda updated version of SNEEP and this time the output file is not empty. I'm now trying to understand what the best strategy is in the case of non-model organisms, a fish in my case. Do you have any advice? Thanks a lot for your help, Best Max

Il giorno lun 18 mar 2024 alle ore 14:17 SchulzLab @.***> ha scritto:

Hello, we were wondering if SNEEP now works for you with the updated bioconda package?

Kind regards, Marcel

— Reply to this email directly, view it on GitHub https://github.com/SchulzLab/SNEEP/issues/8#issuecomment-2003881302, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVMHEKOV4IXG7EM5ED7Z5DYY3SM5AVCNFSM6AAAAABABTCDF2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBTHA4DCMZQGI . You are receiving this because you were mentioned.Message ID: @.***>

-- Massimiliano Babbucci, PhD Department of Comparative Biomedicine and Food Science (BCA) University of Padova Viale dell'Universita' 16, Agripolis I-35020 Legnaro (PD), Italy ORCID: https://orcid.org/0000-0002-4060-4728 Tel: + 39 049 8272506 e-mail: @.***

[BaumgartenNina]

Hi Max,

great to hear that it is working now! Yes sure, I can help you with this, but maybe we can discuss it in another issue? I will just open one ;)

Thanks a lot! Nina