Re: [ccp4bb] Problem in running ARP_WARP in CCP4i...solved....
Dear All, The problem is solved by updating the tcsh version from 6.14.00 to 6.14.17. Thanks to Santosh, Ioan and Lamzin. With regards S. Karthikeyan On 3/7/2013 7:55 PM, Ioan Vancea wrote: Dear Karthikeyan, In order to trace the error may I ask you, please, to change the first line in auto_tracing.sh by adding -x as option to csh: #!/bin/csh -xf and then rerun the command to see where it stops. Cheers, Ioan P.S. I remember that I have seen that kind of error (for shell scripts in general) when the linux PATH/command length is too long. On Mar 7, 2013, at 2:38 PM, S. Karthikeyan wrote: Dear CCP4BB members, I am trying to run arp_warp classic (7.3 version) through ccp4i (CCP4 6.3) in CentOS system. However, it gives the following error even for the example files provided with Arp/Warp. Any suggestions are welcome. --- BFONT COLOR=#FF!--SUMMARY_BEGIN-- QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/warp_tracing.sh !--SUMMARY_END--/FONT/B If I try to run through command line it gives the following error: auto_tracing.sh datafile ../psp.mtz Thu Mar 7 19:09:18 IST 2013 Word too long. QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/auto_tracing.sh --- Thanking you With regards S. Karthikeyan __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- Dr. Ioan Vancea European Molecular Biology Laboratory c/o DESY Notkestrasse 85, 22607 Hamburg, Germany Tel: +49 (0)40 89902-205 Email: ivan...@embl-hamburg.de __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202
[ccp4bb] Problem in running ARP_WARP in CCP4i
Dear CCP4BB members, I am trying to run arp_warp classic (7.3 version) through ccp4i (CCP4 6.3) in CentOS system. However, it gives the following error even for the example files provided with Arp/Warp. Any suggestions are welcome. --- BFONT COLOR=#FF!--SUMMARY_BEGIN-- QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/warp_tracing.sh !--SUMMARY_END--/FONT/B If I try to run through command line it gives the following error: auto_tracing.sh datafile ../psp.mtz Thu Mar 7 19:09:18 IST 2013 Word too long. QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/auto_tracing.sh --- Thanking you With regards S. Karthikeyan __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202
Re: [ccp4bb] Problem in running ARP_WARP in CCP4i
try tcsh auto_tracing.sh datafile ../psp.mtz Santosh Panjikar, Ph.D. Scientist Australian Synchrotron 800 Blackburn Road Clayton VIC 3168 Australia Ph: +61-4-67770815 (mobile) +61-3-85404276 (office) From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of S. Karthikeyan [skart...@imtech.res.in] Sent: Friday, March 08, 2013 12:38 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Problem in running ARP_WARP in CCP4i Dear CCP4BB members, I am trying to run arp_warp classic (7.3 version) through ccp4i (CCP4 6.3) in CentOS system. However, it gives the following error even for the example files provided with Arp/Warp. Any suggestions are welcome. --- BFONT COLOR=#FF!--SUMMARY_BEGIN-- QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/warp_tracing.sh !--SUMMARY_END--/FONT/B If I try to run through command line it gives the following error: auto_tracing.sh datafile ../psp.mtz Thu Mar 7 19:09:18 IST 2013 Word too long. QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/auto_tracing.sh --- Thanking you With regards S. Karthikeyan __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202
Re: [ccp4bb] Problem in running ARP_WARP in CCP4i
Nope, it is not working. Just for information, if I give the command auto_tracing.sh, it prints the 'help' text file... -Karthik On 3/7/2013 7:11 PM, Santosh Panjikar wrote: try tcsh auto_tracing.sh datafile ../psp.mtz Santosh Panjikar, Ph.D. Scientist Australian Synchrotron 800 Blackburn Road Clayton VIC 3168 Australia Ph: +61-4-67770815 (mobile) +61-3-85404276 (office) From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of S. Karthikeyan [skart...@imtech.res.in] Sent: Friday, March 08, 2013 12:38 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Problem in running ARP_WARP in CCP4i Dear CCP4BB members, I am trying to run arp_warp classic (7.3 version) through ccp4i (CCP4 6.3) in CentOS system. However, it gives the following error even for the example files provided with Arp/Warp. Any suggestions are welcome. --- BFONT COLOR=#FF!--SUMMARY_BEGIN-- QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/warp_tracing.sh !--SUMMARY_END--/FONT/B If I try to run through command line it gives the following error: auto_tracing.sh datafile ../psp.mtz Thu Mar 7 19:09:18 IST 2013 Word too long. QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/auto_tracing.sh --- Thanking you With regards S. Karthikeyan __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202
Re: [ccp4bb] Problem in running ARP_WARP in CCP4i
Dear Karthikeyan, In order to trace the error may I ask you, please, to change the first line in auto_tracing.sh by adding -x as option to csh: #!/bin/csh -xf and then rerun the command to see where it stops. Cheers, Ioan P.S. I remember that I have seen that kind of error (for shell scripts in general) when the linux PATH/command length is too long. On Mar 7, 2013, at 2:38 PM, S. Karthikeyan wrote: Dear CCP4BB members, I am trying to run arp_warp classic (7.3 version) through ccp4i (CCP4 6.3) in CentOS system. However, it gives the following error even for the example files provided with Arp/Warp. Any suggestions are welcome. --- BFONT COLOR=#FF!--SUMMARY_BEGIN-- QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/warp_tracing.sh !--SUMMARY_END--/FONT/B If I try to run through command line it gives the following error: auto_tracing.sh datafile ../psp.mtz Thu Mar 7 19:09:18 IST 2013 Word too long. QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/auto_tracing.sh --- Thanking you With regards S. Karthikeyan __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- Dr. Ioan Vancea European Molecular Biology Laboratory c/o DESY Notkestrasse 85, 22607 Hamburg, Germany Tel: +49 (0)40 89902-205 Email: ivan...@embl-hamburg.de
Re: [ccp4bb] Problem in running ARP_WARP in CCP4i
Dear Karthikeyan, It may indeed be too long length of your PATH variable. Can you also type echo $PATH | wc -c and see what the output is? On my Mac it is 641. With best regards, Victor On 07/03/2013 14:38, S. Karthikeyan wrote: Dear CCP4BB members, I am trying to run arp_warp classic (7.3 version) through ccp4i (CCP4 6.3) in CentOS system. However, it gives the following error even for the example files provided with Arp/Warp. Any suggestions are welcome. --- BFONT COLOR=#FF!--SUMMARY_BEGIN-- QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/warp_tracing.sh !--SUMMARY_END--/FONT/B If I try to run through command line it gives the following error: auto_tracing.sh datafile ../psp.mtz Thu Mar 7 19:09:18 IST 2013 Word too long. QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/auto_tracing.sh --- Thanking you With regards S. Karthikeyan __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202
