Crash of clearcut

[yihongchizi]

I am trucking my 1GB miseq data on my computer on Win10 X64, 8GB RAM and 128G SSD + 500G HDD, according to the Miseq SOP. Everything went on very well just till the clearcut command of Phylogenetic step. The mothur immediately crashed every trial when I typed the code and press the enter button. However, I found nothing in the log file that has something to do with the crash, even the entire code of clearcut was not there. What's the hell? What should I do?
PS, the mothur version in use is 1.39.5 win x64

[hanshew]

I'm having this problem too with an old 454 data set. I'm using a series of commands I've used dozens of times before. I enter:
clearcut(phylip=NDRI.final.phylip.dist)
and ever time I get back:
Clearcut: Memory allocation error in NJ_parse_distance_matrix()
Clearcut: Syntax error in distance matrix at offset 7.

I tried v.1.39.5, then I reverted back to v.1.37.4 which has run stable and well for me before. Same problem.
I've reverted

[mothur-westcott]

The clearcut command is very memory intensive. How big is the NDRI.final.phylip.dist file? How much RAM do you have?

[yihongchizi]

Thanks for your kind respond. I've noticed it. My dist file is extremely too big for the RAM. Then how can I go on? Is there any alternative? Thx a ton! 2017-06-24 1:06 GMT+08:00 Sarah Westcott <notifications@github.com>:

…

The clearcut command is very memory intensive. How big is the NDRI.final.phylip.dist file? How much RAM do you have? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#343 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AcBCxPSyWbJ8vERMuH1WTONfzJw54zOOks5sG_B7gaJpZM4N3LI5> .

-- Jie ZHANG Ph.D. candidate Supervisor: Prof. Yahai LU Lab of Soil Microbiology College of Urban and Environmental Sciences, Peking University No. 5, Yiheyuan Road, Haidian District, Beijing 100871, China Telephone No: +86-10-62745939 Cellphone No: (+86) 13164249699 E-mail: joo20141205@gmail.com; zhangjie2014@pku.edu.cn

[hanshew]

I hadn't considered that this is probably the biggest data set I've run. My dist file is 12 GB and I have 8 GB of RAM. I guess I'll have to find someone else to run clearcut for me. Bummer.

[mothur-westcott]

You might be interested in this, https://mothur.org/wiki/Mothur_AMI.

[yihongchizi]

Terribly sorry for replying so late. That's very nice of you for your share. Thanks a ton. Best regards 2017-06-26 21:00 GMT+08:00 Sarah Westcott <notifications@github.com>:

…

You might be interested in this, https://mothur.org/wiki/Mothur_AMI. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#343 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AcBCxNkGgHuq2WWUivk9tEMIySGrHSUhks5sH6tvgaJpZM4N3LI5> .

-- Jie ZHANG Ph.D. candidate Supervisor: Prof. Yahai LU Lab of Soil Microbiology College of Urban and Environmental Sciences, Peking University No. 5, Yiheyuan Road, Haidian District, Beijing 100871, China Telephone No: +86-10-62745939 Cellphone No: (+86) 13164249699 E-mail: joo20141205@gmail.com; zhangjie2014@pku.edu.cn