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Old 08-20-2018, 12:40 AM   #1
TK6009
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Location: Australia

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Default BSmooth error : File name too long

Hi,

I'm currently trying to run the script bsev_sort.pl from BSmooth on my data and I get the following error message:

mkdir CA8R9ANXX_GGCTAC_L003/sorted.pre/bins/____________BC_____T_o_______A____T6____g______U_J_D_T________R___S_______3H____l02___R__4v_BwHq___________N_______v_V_______0___o_____z__m_U_____c8_____A______-m_V________J___b_____E______b___f____2______r___9____Y__9__S___M______6__r___S_9_d_H_____________d_________r__RZ___q_________r__XJ_0J-____O____L_: File name too long at bsmooth-align/bin/../lib/BtlBio/Sort/DiskSort.pm line 434.
Child with PID 2944 exited abnormally at bsmooth-align/bin/disk_sort.pl line 167.
Bad exit level from sort command: 512 at bsmooth-align/bin/bsev_sort.pl line 145.

Same problem when I run it on a example data set created with sim.pl

Any idea what's going wrong and how I can correct it ?
Many thanks !
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Old 08-20-2018, 03:21 AM   #2
Bukowski
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Your file name is too long. Shorten it? Where is that underscore based hell being derived from? If it's coming from the temporary data directory creation try specify a tempdir at execution

Last edited by Bukowski; 08-20-2018 at 03:32 AM.
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Old 08-20-2018, 03:34 AM   #3
TK6009
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Thank you for your reply. The problem is that the files in sorted.pre/bins/ are temporary files created by the script, so I don't control it.
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Old 08-20-2018, 03:59 AM   #4
Bukowski
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Are you running under a job scheduler? I just tried to run the tests, but merman doesn't seem to compile under g++ 5.5.0 - and in fact there's an open issue on that repo that's 3.5 years old, which implies this package is no longer maintained.
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Old 08-20-2018, 07:13 PM   #5
TK6009
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Yes, I'm using a pbs server.
I will find another way to process my data,
Thank you for your time !
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