The index of the first base is less than -2

WGLab / DeepMod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications

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The index of the first base is less than -2 #27

Closed lemonsky123 closed 4 years ago

lemonsky123 commented 4 years ago

Hi @liuqianhn I'm running DeepMod on several fast5 files, and I got the following error Error!!! The index of the first base is less than -2(-12323486=0.000000*4000-12323486) in DEAMERNANOPORE_20161117_FNFAB43577_MN16450_sequencing_run_MA_821_R9_4_NA12878_11_17_16_88738_ch137_read888_strand.fast5 The data was downloaded from NA12878， and was basecalled by Albacore-2.3.1 with the following command read_fast5_basecaller.py --input fast5 --worker 20 --save_path out --flowcell FLO-MIN106 --kit SQK-RAD002 -o fast5 The DeepMod command used is shown below python DeepMod.py detect --wrkBase base_called_fast5 --Ref hg19.fa --FileID test --modfile train_mod/rnn_conmodC_P100wd21_f7ne1u0_4/mod_train_conmodC_P100wd21_f3ne1u0 --threads 15 --outFolder output Could you please tell me where the problem is? Thanks so much! Best.

liuqianhn commented 4 years ago

Hi @lemonsky123 , it seems that there is an issue for the basecalling: no basecalling information or wrong start index for the first event. It will be helpful if you can share "DEAMERNANOPORE_20161117_FNFAB43577_MN16450_sequencing_run_MA_821_R9_4_NA12878_11_17_16_88738_ch137_read888_strand.fast5" with me so that I can check what is the exact issue. Thanks.

lemonsky123 commented 4 years ago

Hi @lemonsky123 , it seems that there is an issue for the basecalling: no basecalling information or wrong start index for the first event. It will be helpful if you can share "DEAMERNANOPORE_20161117_FNFAB43577_MN16450_sequencing_run_MA_821_R9_4_NA12878_11_17_16_88738_ch137_read888_strand.fast5" with me so that I can check what is the exact issue. Thanks.

Hi, @liuqianhn. Thanks for the reply, The fast5 files is shared below. [Uploading DEAMERNANOPORE_20161117_FNFAB43577_MN16450_sequencing_run_MA_821_R9_4_NA12878_11_17_16_88738_ch137_read888_strand.zip…]()

liuqianhn commented 4 years ago

Hi @lemonsky123 , is it very large? It seems that I cannot download it now.

lemonsky123 commented 4 years ago

Hi, @liuqianhn . The file is quite small(about 62KB). I re-upload the file below. Can you download it now? DEAMERNANOPORE_20161117_FNFAB43577_MN16450_sequencing_run_MA_821_R9_4_NA12878_11_17_16_88738_ch137_read888_strand.zip

liuqianhn commented 4 years ago

Hi @lemonsky123 , I can download the new one. Thank you.

lemonsky123 commented 4 years ago

Hi @lemonsky123 , I can download the new one. Thank you.

Nice to hear that, looking forward to hearing from you again.

liuqianhn commented 4 years ago

Hi @lemonsky123 , I re-installed DeepMod and run the command below with your fast5 file under "for_lemonsky123". But I do not get any error.

python DeepMod/bin/DeepMod.py detect --wrkBase for_lemonsky123 --Ref GRCh38/GRCh38.fa --FileID test --modfile DeepMod/train_mod/rnn_conmodC_P100wd21_f7ne1u0_4/mod_train_conmodC_P100wd21_f3ne1u0 --threads 15 --outFolder output

Did you install dependent packages as instructed in "https://github.com/WGLab/DeepMod/blob/master/docs/Install.md"?

lemonsky123 commented 4 years ago

Hi @liuqianhn , Thanks for the reply. I installed all the needed packages with conda accorrding to your tutorial. Then I re-run DeepMod, but I still got the same error. The picture is shown below error

liuqianhn commented 4 years ago

Hi @lemonsky123 , it seems that there are changes in python functions, and some functions do not exist. I have fixed the issue. Could you please download the latest version and have a try? Feel free to let me know if there is any issue.

lemonsky123 commented 4 years ago

Hi, @liuqianhn . I have downloaded the latest version of DeepMod and the error information is gone. Thanks for your help!

lemonsky123 commented 4 years ago

Hi @liuqianhn , when I was using DeepMod for the analysis of 2000 fast5 files, I got the following error: mkdir: cannot create directory ‘××××’: File exists. The picture is shown below pic_20191207204652 But when I reduced the files to 1500, the error was gone, the picture is shown below pic_20191207204709 What's more, another error was also shown in the picture, the error is Error information for different fast5 files: Not in alignment sam ×× Could you please help me with those problems? Thanks so much!

liuqianhn commented 4 years ago

Hi @lemonsky123 , you are fine. The message you are showing does not mean any error in your result.

The first error just means the folder exist and not need to create it.

The second error is to tell you that some reads cannot aligned to the reference genome. On average, you have 5% unmapped reads, which is normal.

In short, your running is without critical error and your result is good.

liuqianhn commented 4 years ago

Closed due to no recent activities.