Error: GEM.System.Error::Signal raised (no=11) [errno=0,Success]

[nchernia]

Hello, I'm trying to run gem-mapper (from the hic tree) on bisulfite data.

I made the index with the "-b" flag.

Here is my command:
./bin/gem-mapper -I Homo_sapiens_assembly19.gem --3c --restriction-enzyme MboI -1 L001_R1_001.fastq.gz -2 L001_R2_001.fastq.gz -o L001_001.sam

I get this error:

2020/6/25 14:49:54 -- [Loading GEM index 'Homo_sapiens_assembly19.gem']
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

GEM.System.Error::Signal raised (no=11) [errno=0,Success]
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

[heathsc]

Hi, Do you have a minimal set of input files that cause the crash that you can share? Thanks. Simon

…

On Thu, Jun 25, 2020 at 9:58 PM nchernia ***@***.***> wrote: Hello, I'm trying to run gem-mapper (from the hic tree) on bisulfite data. I made the index with the "-b" flag. Here is my command: ./bin/gem-mapper -I Homo_sapiens_assembly19.gem --3c --restriction-enzyme MboI -1 L001_R1_001.fastq.gz -2 L001_R2_001.fastq.gz -o L001_001.sam I get this error: 2020/6/25 14:49:54 -- [Loading GEM index 'Homo_sapiens_assembly19.gem'] <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< GEM.System.Error::Signal raised (no=11) [errno=0,Success] <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#17>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAY4655ABONNLB6F4RH3MTDRYOT55ANCNFSM4OIWDG5Q> .

[nchernia]

I can send the fastqs, they are small. Do you want the index? I can send the info file - it looks to me like it created the index with no problem. On Fri, Jun 26, 2020 at 12:49 AM Simon Heath <[email protected]> wrote:

…

Hi, Do you have a minimal set of input files that cause the crash that you can share? Thanks. Simon On Thu, Jun 25, 2020 at 9:58 PM nchernia ***@***.***> wrote: > Hello, I'm trying to run gem-mapper (from the hic tree) on bisulfite data. > > I made the index with the "-b" flag. > > Here is my command: > ./bin/gem-mapper -I Homo_sapiens_assembly19.gem --3c --restriction-enzyme > MboI -1 L001_R1_001.fastq.gz -2 L001_R2_001.fastq.gz -o L001_001.sam > > I get this error: > > 2020/6/25 14:49:54 -- [Loading GEM index 'Homo_sapiens_assembly19.gem'] > > <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< > > GEM.System.Error::Signal raised (no=11) [errno=0,Success] > > <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#17>, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AAY4655ABONNLB6F4RH3MTDRYOT55ANCNFSM4OIWDG5Q > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#17 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAK2EW5T3DLSGDH2XA5JLNLRYQSF3ANCNFSM4OIWDG5Q> .

-- Neva Cherniavsky Durand, Ph.D. Pronouns: she, her, hers Assistant Professor, Aiden Lab www.aidenlab.org

[heathsc]

Just the fastq's should be enough. If I can't reproduce the crash I might ask for a link to the reference file you used. Cheers, Simon

…

On Fri, Jun 26, 2020 at 1:30 PM nchernia ***@***.***> wrote: I can send the fastqs, they are small. Do you want the index? I can send the info file - it looks to me like it created the index with no problem. On Fri, Jun 26, 2020 at 12:49 AM Simon Heath ***@***.***> wrote: > Hi, > > Do you have a minimal set of input files that cause the crash that you can > share? > > Thanks. > Simon > > > On Thu, Jun 25, 2020 at 9:58 PM nchernia ***@***.***> wrote: > > > Hello, I'm trying to run gem-mapper (from the hic tree) on bisulfite > data. > > > > I made the index with the "-b" flag. > > > > Here is my command: > > ./bin/gem-mapper -I Homo_sapiens_assembly19.gem --3c --restriction-enzyme > > MboI -1 L001_R1_001.fastq.gz -2 L001_R2_001.fastq.gz -o L001_001.sam > > > > I get this error: > > > > 2020/6/25 14:49:54 -- [Loading GEM index 'Homo_sapiens_assembly19.gem'] > > > > > <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< > > > > GEM.System.Error::Signal raised (no=11) [errno=0,Success] > > > > > <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< > > > > — > > You are receiving this because you are subscribed to this thread. > > Reply to this email directly, view it on GitHub > > <#17>, or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AAY4655ABONNLB6F4RH3MTDRYOT55ANCNFSM4OIWDG5Q > > > > . > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#17 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AAK2EW5T3DLSGDH2XA5JLNLRYQSF3ANCNFSM4OIWDG5Q > > . > -- Neva Cherniavsky Durand, Ph.D. Pronouns: she, her, hers Assistant Professor, Aiden Lab www.aidenlab.org — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#17 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAY465532IHYM4OWQRCP7KDRYSBGZANCNFSM4OIWDG5Q> .

[nchernia]

I sent them via email. Thanks. On Fri, Jun 26, 2020 at 7:35 AM Simon Heath <[email protected]> wrote:

Just the fastq's should be enough. If I can't reproduce the crash I might ask for a link to the reference file you used. Cheers, Simon On Fri, Jun 26, 2020 at 1:30 PM nchernia ***@***.***> wrote: > I can send the fastqs, they are small. Do you want the index? I can send > the info file - it looks to me like it created the index with no problem. > > On Fri, Jun 26, 2020 at 12:49 AM Simon Heath ***@***.***> > wrote: > > > Hi, > > > > Do you have a minimal set of input files that cause the crash that you > can > > share? > > > > Thanks. > > Simon > > > > > > On Thu, Jun 25, 2020 at 9:58 PM nchernia ***@***.***> > wrote: > > > > > Hello, I'm trying to run gem-mapper (from the hic tree) on bisulfite > > data. > > > > > > I made the index with the "-b" flag. > > > > > > Here is my command: > > > ./bin/gem-mapper -I Homo_sapiens_assembly19.gem --3c > --restriction-enzyme > > > MboI -1 L001_R1_001.fastq.gz -2 L001_R2_001.fastq.gz -o L001_001.sam > > > > > > I get this error: > > > > > > 2020/6/25 14:49:54 -- [Loading GEM index 'Homo_sapiens_assembly19.gem'] > > > > > > > > > <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< > > > > > > GEM.System.Error::Signal raised (no=11) [errno=0,Success] > > > > > > > > > <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< > > > > > > — > > > You are receiving this because you are subscribed to this thread. > > > Reply to this email directly, view it on GitHub > > > <#17>, or unsubscribe > > > < > > > https://github.com/notifications/unsubscribe-auth/AAY4655ABONNLB6F4RH3MTDRYOT55ANCNFSM4OIWDG5Q > > > > > > . > > > > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > < #17 (comment) > >, > > or unsubscribe > > < > https://github.com/notifications/unsubscribe-auth/AAK2EW5T3DLSGDH2XA5JLNLRYQSF3ANCNFSM4OIWDG5Q > > > > . > > > > > -- > Neva Cherniavsky Durand, Ph.D. > Pronouns: she, her, hers > Assistant Professor, Aiden Lab > www.aidenlab.org > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#17 (comment) >, > or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AAY465532IHYM4OWQRCP7KDRYSBGZANCNFSM4OIWDG5Q > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#17 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAK2EWZW27HWCRKIIB4Q4GTRYSBWJANCNFSM4OIWDG5Q> .

-- Neva Cherniavsky Durand, Ph.D. Pronouns: she, her, hers Assistant Professor, Aiden Lab www.aidenlab.org