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smarco / gem3-mapper

GEM-Mapper v3
GNU General Public License v3.0
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Error: GEM.System.Error::Signal raised (no=11) [errno=0,Success] #17

Open nchernia opened 4 years ago

nchernia commented 4 years ago

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 commented 4 years ago

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 notifications@github.com 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 https://github.com/smarco/gem3-mapper/issues/17, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAY4655ABONNLB6F4RH3MTDRYOT55ANCNFSM4OIWDG5Q .

nchernia commented 4 years ago

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 notifications@github.com 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 notifications@github.com 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 https://github.com/smarco/gem3-mapper/issues/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 https://github.com/smarco/gem3-mapper/issues/17#issuecomment-649962983, 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 commented 4 years ago

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 notifications@github.com 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 notifications@github.com 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 notifications@github.com 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 https://github.com/smarco/gem3-mapper/issues/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 <https://github.com/smarco/gem3-mapper/issues/17#issuecomment-649962983 , 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 https://github.com/smarco/gem3-mapper/issues/17#issuecomment-650130864, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAY465532IHYM4OWQRCP7KDRYSBGZANCNFSM4OIWDG5Q .

nchernia commented 4 years ago

I sent them via email. Thanks.

On Fri, Jun 26, 2020 at 7:35 AM Simon Heath notifications@github.com 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 notifications@github.com 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 notifications@github.com 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 notifications@github.com 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 https://github.com/smarco/gem3-mapper/issues/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 < https://github.com/smarco/gem3-mapper/issues/17#issuecomment-649962983 , 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 <https://github.com/smarco/gem3-mapper/issues/17#issuecomment-650130864 , 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 https://github.com/smarco/gem3-mapper/issues/17#issuecomment-650132310, 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