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shilpagarg / DipAsm

MIT License
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gzip: stdout: Broken pipe #17

Closed jenny315 closed 3 years ago

jenny315 commented 3 years ago

hi,

When I run the following command,

/public/home/jenny/software/pstools hic_mapping_unitig -t 60 JT_hifiasm.asm.r_utg.fa <(zcat /public/home/jenny/01data/03hic/clean_data/01big_clean/A1-fastped_R1.fq.gz /public/home/jenny/01data/03hic/clean_data/02small_clean/A1-fastped_R1.fq.gz) <(zcat /public/home/jenny/01data/03hic/clean_data/01big_clean/A1-fastped_R2.fq.gz /public/home/jennyu/01data/03hic/clean_data/02small_clean/A1-fastped_R2.fq.gz)

the following error occurred, I'm working on the first mistake, but I don't understand the second one. The second error look like a problem occued when read from the pipe, I'm not sure。

/public/home/jenny/software/pstools: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /public/home/jenny/software/pstools)
/public/home/jenny/software/pstools: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /public/home/jenny/software/pstools)

gzip: stdout: Broken pipe

gzip: stdout: Broken pipe

I then tried to modify the command (the following), but still reported the same second error.

/public/home/jenny/software/pstools hic_mapping_unitig -t 60 JT_hifiasm.asm.r_utg.fa <(zcat /public/home/jenny/01data/03hic/clean_data/01big_clean/A1_fastped.R1.fq.gz /public/home/jenny/01data/03hic/clean_data/02small_clean/A1_fastped.R1.fq.gz) <(zcat /public/home/jenny/01data/03hic/clean_data/01big_clean/A1_fastped.R2.fq.gz /public/home/jenny/01data/03hic/clean_data/02small_clean/A1_fastped.R2.fq.gz)

and 

/public/home/jenny/software/pstools hic_mapping_unitig -t 60 JT_hifiasm.asm.r_utg.fa <(zcat /public/home/jenny/01data/03hic/clean_data/01big_clean/A1_fastped.R1.fq.gz) <(zcat /public/home/jenny/01data/03hic/clean_data/01big_clean/A1_fastped.R2.fq.gz)

It is OK when I run zcat /public/home/jenny/01data/03hic/clean_data/01big_clean/A1_fastped.R1.fq.gz /public/home/jenny/01data/03hic/clean_data/02small_clean/A1_fastped.R1.fq.gz directly on terminal

When I run commands directly on terminal (manage nodes and subnodes), it‘s OK and only get the first mistake.

/public/home/jenny/software/pstools hic_mapping_unitig -t 1 JT_hifiasm.asm.r_utg.fa <(zcat /public/home/jenny/01data/03hic/clean_data/01big_clean/A1_fastped.R1.fq.gz /public/home/jenny/01data/03hic/clean_data/02small_clean/A1_fastped.R1.fq.gz)  <(zcat /public/home/jenny/01data/03hic/clean_data/01big_clean/A1_fastped.R2.fq.gz /public/home/jenny/01data/03hic/clean_data/02small_clean/A1_fastped.R2.fq.gz)

Error is as follows (just the first mistake)

/public/home/jenny/software/pstools: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /public/home/jenny/software/pstools)
/public/home/jenny/software/pstools: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /public/home/jenny/software/pstools)

But when I put it (command above) in the script and ran it, I got an error.

$ sh pstools4.sh
pstools4.sh: line 1: syntax error near unexpected token `('
pstools4.sh: line 1: `/public/home/jenny/software/pstools hic_mapping_unitig -t 1 JT_hifiasm.asm.r_utg.fa <(zcat /public/home/jenny/01data/03hic/clean_data/01big_clean/A1_fastped.R1.fq.gz /public/home/jenny/01data/03hic/clean_data/02small_clean/A1_fastped.R1.fq.gz)  <(zcat /public/home/jenny/01data/03hic/clean_data/01big_clean/A1_fastped.R2.fq.gz /public/home/jenny/01data/03hic/clean_data/02small_clean/A1_fastped.R2.fq.gz)'

I'm at my wit's end.

GZIP version information

gzip 1.5
Copyright (C) 2007, 2010, 2011 Free Software Foundation, Inc.
Copyright (C) 1993 Jean-loup Gailly.
This is free software.  You may redistribute copies of it under the terms of
the GNU General Public License <http://www.gnu.org/licenses/gpl.html>.
There is NO WARRANTY, to the extent permitted by law.

Thanks for any advice, Best regards, Jenny

shilpagarg commented 3 years ago

Please install proper g++ versions and dependencies, and directly run on real data of human genome.