I see this error when trying to run gemBS map : <d

Yes, it is maintained. I will check this problemSimon <span cla

Hi Simon, Thanks for the reply. Here is the error log I have .. <div class="sn

TypeError: sequence item 15: expected str instance, NoneType found,about heathsc/gembs

Comments (31)

IsmailM commented on August 13, 2024

Changing the below to check against None rather than an empty string ("") fixes the issue for me:

gemBS/gemBS/__init__.py

Lines 723 to 727 in 71e7025

 #Bisulfite Conversion Values 

 if under_conversion != "": 

 mapping.extend(["--underconversion_sequence",under_conversion]) 

 if over_conversion != "": 

 mapping.extend(["--overconversion_sequence",over_conversion])

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PoisonAlien commented on August 13, 2024

Does this repo still maintained ? I have the same issue, and I am wondering if this has been addressed.

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heathsc commented on August 13, 2024

Yes, it is maintained. I will check this problem Simon

…

On Tue, 8 Jan 2019, 09:11 Anand Mayakonda ***@***.*** wrote: Does this repo still maintained ? I have the same issue, and I am wondering if this has been addressed. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPd0qI-rLBUAcjsKLaygp8i2AELN0tks5vBFK7gaJpZM4XAo1t> .

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PoisonAlien commented on August 13, 2024

Hi Simon,
Thanks for the reply. Here is the error log I have ..

: 
: Command map started at 2019-01-08 10:18:43.945975
: 
: ------------ Mapping Parameters ------------
: Sample barcode   : AS-277115-LR-38819
: Data set         : AS-277115-LR-38819
: No. threads      : 2
: Index            : /bigdisk/ref_db/mm10/gemBS/mm10.BS.gem
: Paired           : True
: Read non stranded: True
: Type             : PAIRED
: Input Files      : AS-277115-LR-38819_R1.fastq.gz,AS-277115-LR-38819_R2.fastq.gz
: Output dir       : /mapping/AS-277115-LR-38819
: 
: Bisulfite Mapping...
Traceback (most recent call last):
  File "/usr/local/bin/gemBS", line 11, in <module>
    load_entry_point('gemBS==3.2.2', 'console_scripts', 'gemBS')()
  File "/usr/local/lib/python3.5/dist-packages/gemBS/commands.py", line 157, in gemBS_main
    instances[args.command].run(args)
  File "/usr/local/lib/python3.5/dist-packages/gemBS/production.py", line 367, in run
    self.do_mapping(fl)
  File "/usr/local/lib/python3.5/dist-packages/gemBS/production.py", line 559, in do_mapping
    under_conversion=self.underconversion_sequence,over_conversion=self.overconversion_sequence) 
  File "/usr/local/lib/python3.5/dist-packages/gemBS/__init__.py", line 737, in mapping
    process = run_tools(tools, name="bisulfite-mapping", logfile=logfile)
  File "/usr/local/lib/python3.5/dist-packages/gemBS/utils.py", line 330, in run_tools
    p.start()
  File "/usr/local/lib/python3.5/dist-packages/gemBS/utils.py", line 237, in start
    logging.info("Starting:\n\t%s" % (self.to_bash_pipe()))
  File "/usr/local/lib/python3.5/dist-packages/gemBS/utils.py", line 276, in to_bash_pipe
    return " | ".join([p.to_bash() for p in self.processes])
  File "/usr/local/lib/python3.5/dist-packages/gemBS/utils.py", line 276, in <listcomp>
    return " | ".join([p.to_bash() for p in self.processes])
  File "/usr/local/lib/python3.5/dist-packages/gemBS/utils.py", line 165, in to_bash
    return " ".join(self.commands)
TypeError: sequence item 17: expected str instance, NoneType found

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heathsc commented on August 13, 2024

I pushed a bug fix to github - can you check to see if this fixes your problem? Thanks, Simon

…

On 8 Jan 2019, at 09:21, Anand Mayakonda ***@***.***> wrote: Hi Simon, Thanks for the reply. Here is the error log I have .. : : Command map started at 2019-01-08 10:18:43.945975 : : ------------ Mapping Parameters ------------ : Sample barcode : AS-277115-LR-38819 : Data set : AS-277115-LR-38819 : No. threads : 2 : Index : /bigdisk/ref_db/mm10/gemBS/mm10.BS.gem : Paired : True : Read non stranded: True : Type : PAIRED : Input Files : AS-277115-LR-38819_R1.fastq.gz,AS-277115-LR-38819_R2.fastq.gz : Output dir : /mapping/AS-277115-LR-38819 : : Bisulfite Mapping... Traceback (most recent call last): File "/usr/local/bin/gemBS", line 11, in <module> load_entry_point('gemBS==3.2.2', 'console_scripts', 'gemBS')() File "/usr/local/lib/python3.5/dist-packages/gemBS/commands.py", line 157, in gemBS_main instances[args.command].run(args) File "/usr/local/lib/python3.5/dist-packages/gemBS/production.py", line 367, in run self.do_mapping(fl) File "/usr/local/lib/python3.5/dist-packages/gemBS/production.py", line 559, in do_mapping under_conversion=self.underconversion_sequence,over_conversion=self.overconversion_sequence) File "/usr/local/lib/python3.5/dist-packages/gemBS/__init__.py", line 737, in mapping process = run_tools(tools, name="bisulfite-mapping", logfile=logfile) File "/usr/local/lib/python3.5/dist-packages/gemBS/utils.py", line 330, in run_tools p.start() File "/usr/local/lib/python3.5/dist-packages/gemBS/utils.py", line 237, in start logging.info("Starting:\n\t%s" % (self.to_bash_pipe())) File "/usr/local/lib/python3.5/dist-packages/gemBS/utils.py", line 276, in to_bash_pipe return " | ".join([p.to_bash() for p in self.processes]) File "/usr/local/lib/python3.5/dist-packages/gemBS/utils.py", line 276, in <listcomp> return " | ".join([p.to_bash() for p in self.processes]) File "/usr/local/lib/python3.5/dist-packages/gemBS/utils.py", line 165, in to_bash return " ".join(self.commands) TypeError: sequence item 17: expected str instance, NoneType found — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPdx09zroRqqNLXElkIW50uUuoPtDRks5vBFT9gaJpZM4XAo1t>.

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PoisonAlien commented on August 13, 2024

Hi Simon,
Thanks for the quick fix. Alignment went smoothly, however I have new error in BScall.. Below is the log..

$ gemBS call
: 
: Command call started at 2019-01-08 12:24:02.381098
: 
: ----------- Methylation Calling --------
: Reference       : /bigdisk/scJens/gem_bs/genome/mm10.fa
: Species         : mm10
: Right Trim      : 10
: Left Trim       : 10
: Chromosomes     : ['chr1', 'chr2', 'chrX', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr10', 'chr8', 'chr14', 'chr9', 'chr11', 'chr13', 'chr12', 'chr15', 'chr16', 'chr17', 'chrY', 'chr18', 'chr19', '@pool_1']
: Threads         : 6
: Sample: AS-277115-LR-38819    Bam: /bigdisk/scJens/gem_bs//mapping/AS-277115-LR-38819/AS-277115-LR-38819.bam
: 
: Methylation Calling...
2019-01-08 12:25:06,267 ERROR: Process '/home/epicwl/miniconda3/lib/python3.6/site-packages/gemBS/gemBSbinaries/bs_call' finished with 1
2019-01-08 12:25:06,267 ERROR: Loading reference sequences
2019-01-08 12:25:06,267 ERROR: Completed loading reference sequences
2019-01-08 12:25:06,267 ERROR: Processing chromosome chr2 (OK)
2019-01-08 12:25:06,267 ERROR: > System.Error::Signal raised (no=11)
Exception in thread Thread-2:
Traceback (most recent call last):
ValueError: Error while executing the bscall process.

And the above error just hangs, I had to terminate the process.

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heathsc commented on August 13, 2024

OK, this is not good! Anyway I can get access to the files so that I can try and reproduce the error on my system? Simon

…

On 8 Jan 2019, at 11:30, Anand Mayakonda ***@***.***> wrote: Hi Simon, Thanks for the quick fix. Alignment went smoothly, however I have new error in BScall.. Below is the log.. : : Command call started at 2019-01-08 12:24:02.381098 : : ----------- Methylation Calling -------- : Reference : /bigdisk/scJens/gem_bs/genome/mm10.fa : Species : mm10 : Right Trim : 10 : Left Trim : 10 : Chromosomes : ['chr1', 'chr2', 'chrX', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr10', 'chr8', 'chr14', 'chr9', 'chr11', 'chr13', 'chr12', 'chr15', 'chr16', 'chr17', 'chrY', 'chr18', 'chr19', ***@***.***_1'] : Threads : 6 : Sample: AS-277115-LR-38819 Bam: /bigdisk/scJens/gem_bs//mapping/AS-277115-LR-38819/AS-277115-LR-38819.bam : : Methylation Calling... 2019-01-08 12:25:06,267 ERROR: Process '/home/epicwl/miniconda3/lib/python3.6/site-packages/gemBS/gemBSbinaries/bs_call' finished with 1 2019-01-08 12:25:06,267 ERROR: Loading reference sequences 2019-01-08 12:25:06,267 ERROR: Completed loading reference sequences 2019-01-08 12:25:06,267 ERROR: Processing chromosome chr2 (OK) 2019-01-08 12:25:06,267 ERROR: > System.Error::Signal raised (no=11) Exception in thread Thread-2: Traceback (most recent call last): ValueError: Error while executing the bscall process. And the above error just hangs, I had to terminate the process. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPd16f4s64p23eZaaght0TVTO32XTZks5vBHNcgaJpZM4XAo1t>.

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PoisonAlien commented on August 13, 2024

Do you need fastq files or the bam file ?

Also this is a single cell library with non-directional protocol. I quickly did map-report and it says 33% overall alignment rate before deduplication (attached). For same sample when I used Bismark it reported ~18% alignment.

AS-277115-LR-38819.html.zip

While you take a look at the error, could you suggest me if I can use any downstream tools deduplication (is picard fine?) and for methylation extraction ?

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heathsc commented on August 13, 2024

Just the BAM should be fine. Which reference are you using? Normally deduplication is not required (it is performed by the caller). If you could send a copy of the parameters files you are using for gemBS that would be helpful. Thanks, Simon

…

On 8 Jan 2019, at 11:45, Anand Mayakonda ***@***.***> wrote: Do you need fastq files or the bam file ? Also this is a single cell library with non-directional protocol. I quickly did map-report and it says 33% overall alignment rate before deduplication (attached). For same sample when I used Bismark it reported ~18% alignment. AS-277115-LR-38819.html.zip <https://github.com/heathsc/gemBS/files/2736357/AS-277115-LR-38819.html.zip> While you take a look at the error, could you suggest me if I can use any downstream tools deduplication (is picard fine?) and for methylation extraction ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPdxtQd0fy2hLX_gXUTdpCxZ_5aa9oks5vBHbdgaJpZM4XAo1t>.

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PoisonAlien commented on August 13, 2024

Here
scbs_samples.conf.zip

Could you please let me know once you download the file so that I can remove it from the Dropbox.
Thank you and hope this helps. Also is it ok to use MethylDackel for extraction ?

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heathsc commented on August 13, 2024

OK, I have the files. I’ll let you know how I get on with testing. I have no experience with MethylDackel. As far as I can see it does not take account of any possible sequence variation so the output should be treated with caution. I’m not sure how well it will work with BAMs generated from gemBS - it depends whether it recognizes the tags in the BAM file that describe the bisulfite strand. All bisulfite mappers use different tags for this (bs_call understands the BAMs from about 5 different mappers). Simon

…

On 8 Jan 2019, at 12:23, Anand Mayakonda ***@***.***> wrote: Here <https://www.dropbox.com/s/047fjs49teb1zmc/AS-277115-LR-38819.bam?dl=0> scbs_samples.conf.zip <https://github.com/heathsc/gemBS/files/2736506/scbs_samples.conf.zip> Could you please let me know once you download the file so that I can remove it from the Dropbox. Thank you and hope this helps. Also is it ok to use MethylDackel for extraction ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPdxz-yH3JlcH3e_1c6_FRZlFJkgp4ks5vBH-0gaJpZM4XAo1t>.

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PoisonAlien commented on August 13, 2024

Ah! Got it. Thank you.

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heathsc commented on August 13, 2024

The calling for your files runs without problems on my system. How did you install gemBS? Would it be possible to try the Docker or Singularity containers to see if these work for you? Simon

…

On 8 Jan 2019, at 13:48, Anand Mayakonda ***@***.***> wrote: Ah! Got it. Thank you. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPdwt-cF4onzWMk02n9uzvoXXDcQr5ks5vBJORgaJpZM4XAo1t>.

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PoisonAlien commented on August 13, 2024

I followed the instructions as in the docs for installation.

git clone --recursive https://github.com/heathsc/gemBS.git
python3 setup.py install

I do not have experience with docker/singularity but I see there are instructions in the docs. I will try it and let you know.

Thank you for the help.

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heathsc commented on August 13, 2024

Should be OK then - what type of computer are you running this on (CPU, memory, OS etc.) ? Simon

…

On 8 Jan 2019, at 16:15, Anand Mayakonda ***@***.***> wrote: I followed the instructions as in the docs for installation. git clone --recursive https://github.com/heathsc/gemBS.git python3 setup.py install I do not have experience with docker/singularity but I see there are instructions in the docs. I will try it and let you know. Thank you for the help. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPdyCFFD7kTS15pc-4Q3x2IRyrPui6ks5vBLX6gaJpZM4XAo1t>.

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PoisonAlien commented on August 13, 2024

I am running it on a local system with 128G RAM and 20 threads running on Ubuntu 16.04 LTS.
I just installed it on another system, will let you know if I face the same issuse..

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heathsc commented on August 13, 2024

That should be more than enough and Ubuntu 16.04 is a tested system. If you re-run the calling with less threads does it make a difference (it shouldn’t do, but I’m trying to pinpoint what could be triggering the bug). Simon

…

On 8 Jan 2019, at 16:37, Anand Mayakonda ***@***.***> wrote: I am running it on a local system with 128G RAM and 20 threads running on Ubuntu 16.04 LTS. I just installed it on another system, will let you know if I face the same issuse.. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPd3mR-7Cg4mhq-XYxobI6WZv7Y-Zyks5vBLs4gaJpZM4XAo1t>.

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PoisonAlien commented on August 13, 2024

Okay, I will check. Should I start with the alignment ? Or is there a way to use just 1 thread for gemBS call, since the config file has been set to 6 threads.

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heathsc commented on August 13, 2024

Just the calling. Maybe set it to 1 thread to see if it runs through. Simon

…

On 8 Jan 2019, at 16:44, Anand Mayakonda ***@***.***> wrote: Okay, I will check. Should I start with the alignment ? Or is there a way to use just 1 thread for gemBS call, since the config file has been set to 6 threads. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPd8erVJS4-Nncei8FxFwkvgyQbtRyks5vBLzogaJpZM4XAo1t>.

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PoisonAlien commented on August 13, 2024

Nope, still the same issue. I changed threads valueto 1 in .gemBS/gemBS.json and ran the command.

 gemBS call
: 
: Command call started at 2019-01-08 18:00:30.938804
: 
: ----------- Methylation Calling --------
: Reference       : /bigdisk/scJens/gem_bs/genome/mm10.fa
: Species         : mm10
: Right Trim      : 10
: Left Trim       : 10
: Chromosomes     : ['chr1', 'chr2', 'chrX', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr10', 'chr8', 'chr14', 'chr9', 'chr11', 'chr13', 'chr12', 'chr15', 'chr16', 'chr17', 'chrY', 'chr18', 'chr19', '@pool_1']
: Threads         : 1
: Sample: AS-277115-LR-38819    Bam: /bigdisk/scJens/gem_bs//mapping/AS-277115-LR-38819/AS-277115-LR-38819.bam
: 
: Methylation Calling...
2019-01-08 18:01:08,477 ERROR: Process '/home/epicwl/miniconda3/lib/python3.6/site-packages/gemBS/gemBSbinaries/bs_call' finished with 1
2019-01-08 18:01:08,478 ERROR: Loading reference sequences
2019-01-08 18:01:08,478 ERROR: Completed loading reference sequences
2019-01-08 18:01:08,478 ERROR: Processing chromosome chr7 (OK)
2019-01-08 18:01:08,478 ERROR: > System.Error::Signal raised (no=11)
Exception in thread Thread-2:
Traceback (most recent call last):
ValueError: Error while executing the bscall process.

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heathsc commented on August 13, 2024

And this happens straightaway after the line 'Processing chromosome chr7 (OK)’ is printed? Simon

…

On 8 Jan 2019, at 17:04, Anand Mayakonda ***@***.***> wrote: Nope, still the same issue. I changed threads valueto 1 in .gemBS/gemBS.json and ran the command. gemBS call : : Command call started at 2019-01-08 18:00:30.938804 : : ----------- Methylation Calling -------- : Reference : /bigdisk/scJens/gem_bs/genome/mm10.fa : Species : mm10 : Right Trim : 10 : Left Trim : 10 : Chromosomes : ['chr1', 'chr2', 'chrX', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr10', 'chr8', 'chr14', 'chr9', 'chr11', 'chr13', 'chr12', 'chr15', 'chr16', 'chr17', 'chrY', 'chr18', 'chr19', ***@***.***_1'] : Threads : 1 : Sample: AS-277115-LR-38819 Bam: /bigdisk/scJens/gem_bs//mapping/AS-277115-LR-38819/AS-277115-LR-38819.bam : : Methylation Calling... 2019-01-08 18:01:08,477 ERROR: Process '/home/epicwl/miniconda3/lib/python3.6/site-packages/gemBS/gemBSbinaries/bs_call' finished with 1 2019-01-08 18:01:08,478 ERROR: Loading reference sequences 2019-01-08 18:01:08,478 ERROR: Completed loading reference sequences 2019-01-08 18:01:08,478 ERROR: Processing chromosome chr7 (OK) 2019-01-08 18:01:08,478 ERROR: > System.Error::Signal raised (no=11) Exception in thread Thread-2: Traceback (most recent call last): ValueError: Error while executing the bscall process. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPd0g6KAS6hUVgndwv3CUUJycB8w_Mks5vBMGbgaJpZM4XAo1t>.

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PoisonAlien commented on August 13, 2024

Its weird. Every time I run gemBS call it stops at the next chromosome.

: Methylation Calling...
2019-01-08 18:10:16,045 ERROR: Process '/home/epicwl/miniconda3/lib/python3.6/site-packages/gemBS/gemBSbinaries/bs_call' finished with 1
2019-01-08 18:10:16,045 ERROR: Loading reference sequences
2019-01-08 18:10:16,045 ERROR: Completed loading reference sequences
2019-01-08 18:10:16,045 ERROR: Processing chromosome chr10 (OK)
2019-01-08 18:10:16,046 ERROR: > System.Error::Signal raised (no=11)
Exception in thread Thread-1:
Traceback (most recent call last):
ValueError: Error while executing the bscall process.

2019-01-08 18:10:16,083 ERROR: Process '/home/epicwl/miniconda3/lib/python3.6/site-packages/gemBS/gemBSbinaries/bs_call' finished with 1
2019-01-08 18:10:16,083 ERROR: Loading reference sequences
2019-01-08 18:10:16,083 ERROR: Completed loading reference sequences
2019-01-08 18:10:16,083 ERROR: Processing chromosome chr8 (OK)
2019-01-08 18:10:16,083 ERROR: > System.Error::Signal raised (no=11)
Exception in thread Thread-2:
Traceback (most recent call last):
ValueError: Error while executing the bscall process.

: Methylation call done, samples performed: AS-277115-LR-38819

I also think its still using more than one thread. How do I force it to use single thread ?

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heathsc commented on August 13, 2024

Is it completing the chromosomes each time? If you look in the calling directory, do you see a bcf file and a json file for the chromosome (particularly the json file, as this is only generated at the end)?

…

On 8 Jan 2019, at 17:12, Anand Mayakonda ***@***.***> wrote: Its weird. Every time I run gemBS call it stops at the next chromosome. : Methylation Calling... 2019-01-08 18:10:16,045 ERROR: Process '/home/epicwl/miniconda3/lib/python3.6/site-packages/gemBS/gemBSbinaries/bs_call' finished with 1 2019-01-08 18:10:16,045 ERROR: Loading reference sequences 2019-01-08 18:10:16,045 ERROR: Completed loading reference sequences 2019-01-08 18:10:16,045 ERROR: Processing chromosome chr10 (OK) 2019-01-08 18:10:16,046 ERROR: > System.Error::Signal raised (no=11) Exception in thread Thread-1: Traceback (most recent call last): ValueError: Error while executing the bscall process. 2019-01-08 18:10:16,083 ERROR: Process '/home/epicwl/miniconda3/lib/python3.6/site-packages/gemBS/gemBSbinaries/bs_call' finished with 1 2019-01-08 18:10:16,083 ERROR: Loading reference sequences 2019-01-08 18:10:16,083 ERROR: Completed loading reference sequences 2019-01-08 18:10:16,083 ERROR: Processing chromosome chr8 (OK) 2019-01-08 18:10:16,083 ERROR: > System.Error::Signal raised (no=11) Exception in thread Thread-2: Traceback (most recent call last): ValueError: Error while executing the bscall process. : Methylation call done, samples performed: AS-277115-LR-38819 I also think its still using more than one thread. How do I force it to use single thread ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPdykpXWVJldwVUUWv5dMtKALzYCUPks5vBMNwgaJpZM4XAo1t>.

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PoisonAlien commented on August 13, 2024

Yes, there are json and bcf files for the ones that are completed. But all the json files are empty.

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PoisonAlien commented on August 13, 2024

Okay, on a different system it works fine and calling completed without any error. I guess it was an installation problem on the main system. Thank you for your patient replies and apologies for the mess :|
Should have checked it properly.

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heathsc commented on August 13, 2024

Thanks for the feedback, but a segfault is never good and I would be happier knowing what caused it! If you get around to re-installing gemBS on the original system, please let me know if it works (and definitely if it still does not work!). Simon

…

On 8 Jan 2019, at 17:46, Anand Mayakonda ***@***.***> wrote: Okay, on a different system it works fine and calling completed without any error. I guess it was an installation problem on the main system. Thank you for your patient replies and apologies for the mess :| Should have checked it properly. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPdxiL1y5po8Eiz3RVPHYXtqAAGqKTks5vBMtjgaJpZM4XAo1t>.

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PoisonAlien commented on August 13, 2024

Sure. Tomorrow I will check again and update you. Thanks again.

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PoisonAlien commented on August 13, 2024

Hi Simon,
I reinstalled everything on the new system and it worked fine. Still dont know how it messed up the first installation.

I have another question to ask. How do I run gemBS map with a custom input json file ?

$gemBS prepare -c ${conf} -t ${csv} --output ${sample_name}.json --no-db
$gemBS map 
gemBS.utils.CommandException: gemBS JSON file not found.

How do I pass output json from prepare command to map command ?

Thanks again.

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heathsc commented on August 13, 2024

To pass a custom json file, use the -j command line option *before* the subcommand so: gemBS -j myfile.json map Simon

…

On 9 Jan 2019, at 15:35, Anand Mayakonda ***@***.***> wrote: Hi, Simon, I reinstalled everything on the new system and it worked fine. Still dont know how it messed up the first installation. I have another question to ask. How do I run gemBS map with a custom input json file ? $gemBS prepare -c ${conf} -t ${csv} --output ${sample_name}.json --no-db $gemBS map gemBS.utils.CommandException: gemBS JSON file not found. How do I pass output json from prepare command to map command ? Thanks again. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#37 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADHPd7ncBK7SCbgmCq55mYRYvOXOKO_fks5vBf4agaJpZM4XAo1t>.

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PoisonAlien commented on August 13, 2024

Ah! Nice. It works. I was using the wrong way then gemBS map -j myfile.json

Thanks again.

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IsmailM commented on August 13, 2024

Thanks for fixing this @heathsc 👍

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TypeError: sequence item 15: expected str instance, NoneType found about gembs HOT 31 CLOSED

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	#Bisulfite Conversion Values
	if under_conversion != "":
	mapping.extend(["--underconversion_sequence",under_conversion])
	if over_conversion != "":
	mapping.extend(["--overconversion_sequence",over_conversion])