Cann't get the cns.fasta

[shehongbing]

HI, there are 20 get_cns** directory but only in get_cns01 directory that I can not get the cns.fasta. and the nextDenovo.sh.e shown is following:

/ifs1/User/shehongbing/zhuang/next/n02/01_rundir_yy/02.cns_align/01.get_cns.sh.work/get_cns01/nextDenovo.sh: 行 5: 448178 段错误 python /ifs1/User/shehongbing/soft/NextDenov o/lib/nextcorrect.py -f /ifs1/User/shehongbing/zhuang/next/n02/01_rundir_yy/02.cns_align//01.get_cns.input.idxs -i /ifs1/User/shehongbing/zhuang/next/n02/01_rundir_yy/01.raw_align/03.sort _align.sh.work/sort_align01/input.seed.002.sorted.ovl -p 7 -max_lq_length 10000 -o cns.fasta

but I compare the nextDenove.sh with others in get_cns03 directory, actually, its no mistakes at all.

[moold]

What is your NextDenovo version?

[shehongbing]

v2.1-beta.0. others could word correctly except get_cns01

在 2019年11月21日，上午10:05，Hu Jiang notifications@github.com 写道：

What is your NextDenovo version?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nextomics/NextDenovo/issues/32?email_source=notifications&email_token=ALZETBLSMIZHLVMB7ZV2QDDQUXUGZA5CNFSM4JP3XHT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEYKGGA#issuecomment-556835608, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALZETBIRXN3DBBDMMTIEJLDQUXUGZANCNFSM4JP3XHTQ.

[moold]

It seems some errors in this file, /ifs1/User/shehongbing/zhuang/next/n02/01_rundir_yy/01.raw_align/03.sort _align.sh.work/sort_align01/input.seed.002.sorted.ovl, you can try to rerun this task:/ifs1/User/shehongbing/zhuang/next/n02/01_rundir_yy/01.raw_align/03.sort _align.sh.work/sort_align01/*sh, but pls rerun its corresponding minimap2 tasks first to prepare its input.

[shehongbing]

Thank you, I’ll try it

在 2019年11月21日，上午10:19，Hu Jiang notifications@github.com 写道：

It seems some errors in this file, /ifs1/User/shehongbing/zhuang/next/n02/01_rundir_yy/01.raw_align/03.sort _align.sh.work/sort_align01/input.seed.002.sorted.ovl , you can try to rerun this task:/ifs1/User/shehongbing/zhuang/next/n02/01_rundir_yy/01.raw_align/03.sort _align.sh.work/sort_align01/*sh, but pls rerun its corresponding minimap2 tasks first to prepare its input.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nextomics/NextDenovo/issues/32?email_source=notifications&email_token=ALZETBOFFORRUF5BRD2Q74LQUXV2BA5CNFSM4JP3XHT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEYNKUI#issuecomment-556848465, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALZETBM63TS6DJCIFOSFPX3QUXV2BANCNFSM4JP3XHTQ.

[shehongbing]

Hi, it dose work correctly. thank you Dr. Hu. And I have another question. raw data and corrected data (by canu), which is better for NextDenovo

[moold]

For another question, you should open a new issue.