ARB Crashes with reduced tree

[guest]

Good day,

I am running Arb 7.0 on macOS Monterey version 12.4, 8GB of memory, installed via Homebrew.

I am trying to create a reduced from the SILVA SSU database's by..

1. Adding in my own sequences to the via quick add parsimony
2. Keeping marked sequences from the genus that aligns with my added sequences, then unmarking everything
3. Removing marked sequences that are redundant or low-quality to thin out the .

I have saved the database as separate files for the original database and each step. I've found that I am now getting the following error when attempting to remove more marked sequences from the :

(base) name@MacBook-Pro-2 ~ % arb                                            
Using ARBHOME='/usr/local/Cellar/arb@7/7.0.1'                                          
Using properties from /Users/name/.arb_prop                                  
Please wait while the program ARB is starting .....                                    
Waiting for '/Users/name/.arb_tmp/sockets/arb_launcher.10641'..              
[arb_launcher[0]: log for ARB_PID='10641']                                             
Tue  2 Aug 2022 15:51:19 MDT arb server.log created by arb_launcher                    
[arb_launcher[0]: Starting 'arb_ntree'..]                                              
Using properties from '/usr/local/Cellar/arb@7/7.0.1/lib/arb_default/ntree.arb'        
Using properties from '/usr/local/Cellar/arb@7/7.0.1/lib/arb_default/status.arb'       
limited resource 3 to 20971520 (was: 8388608 of 67104768)                              
ARB: Loading 'ntree.arb'                                                               
ARB: Loading '/usr/local/Cellar/arb@7/7.0.1/lib/arb_default/ntree.arb' done            

ARB: ARB: Loading '/Users/name/Downloads/ARB_Working_Directory/16S_Syn       echococcus_Tree_Trimmed2.arb'                                                          
ARB: ARB: no FastLoad File '/Users/name/Downloads/ARB_Working_Director       y/16S_Synechococcus_Tree_Trimmed2.ARM' found => loading entire DB                      
ARB: ARB: Loading '/Users/name/Downloads/ARB_Working_Directory/16S_Syn       echococcus_Tree_Trimmed2.arb' done                                                     

[Action: `arb_macro_compatibility.sh &`]                                               
Progress: Loading database                                                             
ARB: no FastLoad File '/usr/local/Cellar/arb@7/7.0.1/demo.ARM' found => loading        entire DB                                                                              
...................................................................... [100.0%]        used: 0s                                                                               
[done]                                                                                 
Number of species in database: 100                                                     
/usr/local/Cellar/arb@7/7.0.1/libexec/arb_launcher: line 25: 10698 Killed: 9               $CMD
[arb_launcher[0]: 'arb_ntree' has terminated with error 137]
[arb_launcher[0]: All launched processes terminated]
[arb_launcher[0]: cleaning up arb session]
  PID TTY           TIME CMD
rmdir: /Users/name/.arb_prop/logs/20220802_155119.10657: Directory not empty

Session log has been stored in /Users/name/.arb_prop/logs/session.20220802_155119.10657.tgz
    and is also accessible via /Users/name/ARB_last_session.tgz

ARB crashed :-(

Additionally now, when I try to load that .arb file or others, I get the following error and am unable to open any .arb files:

Using ARBHOME='/usr/local/Cellar/arb@7/7.0.1'
Using properties from /Users/name/.arb_prop
Please wait while the program ARB is starting .....
Waiting for '/Users/name/.arb_tmp/sockets/arb_launcher.10989'..
Tue  2 Aug 2022 16:05:12 MDT arb server.log created by arb_launcher
[arb_launcher[0]: log for ARB_PID='10989']
[arb_launcher[0]: Starting 'arb_ntree'..]
Using properties from '/usr/local/Cellar/arb@7/7.0.1/lib/arb_default/ntree.arb'
Using properties from '/usr/local/Cellar/arb@7/7.0.1/lib/arb_default/status.arb'
limited resource 3 to 20971520 (was: 8388608 of 67104768)
/usr/local/Cellar/arb@7/7.0.1/libexec/arb_launcher: line 25: 11046 Killed: 9               $CMD
[arb_launcher[0]: 'arb_ntree' has terminated with error 137]
[arb_launcher[0]: All launched processes terminated]
[arb_launcher[0]: cleaning up arb session]
  PID TTY           TIME CMD
rmdir: /Users/name/.arb_prop/logs/20220802_160512.11005: Directory not empty

Session log has been stored in /Users/name/.arb_prop/logs/session.20220802_160512.11005.tgz
    and is also accessible via /Users/name/ARB_last_session.tgz

ARB crashed :-(

I haven't been able to find any information on this arb_ntree error 137 on the wiki or otherwise. I'm a novice with Arb and am unsure how I could have seemingly broken my databases. I would really appreciate any ideas anyone has on how to resolve this.

[westram]

Could you please send me the two session-logs

• ~/.arb_prop/logs/session.20220802_155119.10657.tgz and
• ~/.arb_prop/logs/session.20220802_160512.11005.tgz

preferable via mail to devel@…, because they contain private information from your useraccount, you might not want to share with the public.

Please also test to run arb with the demo.arb database delivered with arb. You'll find that file in directory /usr/local/Cellar/arb@7/7.0.1/

Best wishes, Ralf

[westram]

This issue was caused by lack of space on the drive containing the database.