NanoPlot crash on openSUSE

Question

NanoPlot crash on openSUSE

gwaldbieser opened this issue 7 years ago · 2 comments

Trying to upgrade nanopack on the openSUSE box

$ cat /etc/*-release
NAME="openSUSE Leap"
VERSION="42.3"
ID=opensuse
ID_LIKE="suse"
VERSION_ID="42.3"
PRETTY_NAME="openSUSE Leap 42.3"
ANSI_COLOR="0;32"
CPE_NAME="cpe:/o:opensuse:leap:42.3"
BUG_REPORT_URL="https://bugs.opensuse.org"
HOME_URL="https://www.opensuse.org/"
openSUSE 42.3 (x86_64)
VERSION = 42.3
CODENAME = Malachite

$ python -V
Python 3.5.2 :: Anaconda custom (64-bit)
#########################################
NanoPlot ran but gave an error.
I uninstalled nanopack, NanoPlot, NanoLyse, NanoComp, NanoFilt and NanoStat and started from scratch.
#########################################
$ pip install nanopack
Collecting nanopack
Collecting NanoStat>=0.6.1 (from nanopack)
Requirement already satisfied: NanoGUI in /root/anaconda3/lib/python3.5/site-packages (from nanopack)
Collecting NanoPlot>=0.20.1 (from nanopack)
Requirement already satisfied: nanoget>=0.15.0 in /root/anaconda3/lib/python3.5/site-packages (from nanopack)
Collecting NanoFilt>=1.5.2 (from nanopack)
Requirement already satisfied: nanomath>=0.13.3 in /root/anaconda3/lib/python3.5/site-packages (from nanopack)
Collecting NanoLyse>=0.2.1 (from nanopack)
Requirement already satisfied: nanoplotter>=0.16.5 in /root/anaconda3/lib/python3.5/site-packages (from nanopack)
Collecting NanoComp>=0.4.0 (from nanopack)
Requirement already satisfied: numpy in /root/anaconda3/lib/python3.5/site-packages (from NanoPlot>=0.20.1->nanopack)
Requirement already satisfied: scipy in /root/anaconda3/lib/python3.5/site-packages (from NanoPlot>=0.20.1->nanopack)
Requirement already satisfied: python-dateutil in /root/anaconda3/lib/python3.5/site-packages (from NanoPlot>=0.20.1->nanopack)
Requirement already satisfied: pysam>0.10.0.0 in /root/anaconda3/lib/python3.5/site-packages (from NanoPlot>=0.20.1->nanopack)
Requirement already satisfied: seaborn in /root/anaconda3/lib/python3.5/site-packages (from NanoPlot>=0.20.1->nanopack)
Requirement already satisfied: biopython in /root/anaconda3/lib/python3.5/site-packages (from NanoPlot>=0.20.1->nanopack)
Requirement already satisfied: pandas>=0.22.0 in /root/anaconda3/lib/python3.5/site-packages (from NanoPlot>=0.20.1->nanopack)
Requirement already satisfied: mappy>=2.2 in /root/anaconda3/lib/python3.5/site-packages (from NanoLyse>=0.2.1->nanopack)
Requirement already satisfied: matplotlib>=2.0.0 in /root/anaconda3/lib/python3.5/site-packages (from nanoplotter>=0.16.5->nanopack)
Requirement already satisfied: pauvre in /root/anaconda3/lib/python3.5/site-packages (from nanoplotter>=0.16.5->nanopack)
Requirement already satisfied: six>=1.5 in /root/anaconda3/lib/python3.5/site-packages (from python-dateutil->NanoPlot>=0.20.1->nanopack)
Requirement already satisfied: pytz>=2011k in /root/anaconda3/lib/python3.5/site-packages (from pandas>=0.22.0->NanoPlot>=0.20.1->nanopack)
Requirement already satisfied: cycler>=0.10 in /root/anaconda3/lib/python3.5/site-packages (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /root/anaconda3/lib/python3.5/site-packages (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)
Requirement already satisfied: kiwisolver>=1.0.1 in /root/anaconda3/lib/python3.5/site-packages (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)
Requirement already satisfied: setuptools in /root/anaconda3/lib/python3.5/site-packages (from kiwisolver>=1.0.1->matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)
Installing collected packages: NanoStat, NanoPlot, NanoFilt, NanoLyse, NanoComp, nanopack
Successfully installed NanoComp-0.15.0 NanoFilt-2.0.1 NanoLyse-0.5.1 NanoPlot-1.10.5 NanoStat-1.1.0 nanopack-1.0.0
$ NanoComp -v
NanoComp 0.15.0
$ NanoPlot -v
NanoPlot 1.10.5
$ NanoLyse -v
NanoLyse 0.5.1
$ NanoFilt -v
NanoFilt 2.0.1
$ NanoStat -v
NanoStat 1.1.0
#######################################
##Ran Nanoplot on your test data
$ NanoPlot -t 32 --fastq reads.fastq.gz --N50 --loglength -o Plot1 &
NanoPlot_20180310_1339.log

##These files are produced then it crashes.
HistogramReadlength.png
Log_LengthvsQualityScatterPlot_dot.png
LogTransformed_HistogramReadlength.png
NanoPlot_20180310_1339.log
NanoStats.txt
Weighted_HistogramReadlength.png
Weighted_LogTransformed_HistogramReadlength.png

#Log file
NanoPlot_20180310_1339.log

Answer 1 · 2018-03-10T20:34:58.000Z

I believe this is a duplicate of wdecoster/NanoPlot#21, can you confirm?

In my opinion this is a seaborn issue, and not NanoPlot itself. I will raise this on the seaborn github and see if they are willing to fix this, if not I shall fix it in NanoPlot.

Cheers,
Wouter

Answer 2 · 2018-03-10T21:06:27.000Z

Looks like it. Thanks. Sent from my Android phone using TouchDown (www.symantec.com)

…

-----Original Message----- From: Wouter De Coster [notifications@github.com] Received: Saturday, 10 Mar 2018, 2:35pm To: wdecoster/nanopack [nanopack@noreply.github.com] CC: Waldbieser, Geoff [Geoff.Waldbieser@ARS.USDA.GOV]; Author [author@noreply.github.com] Subject: Re: [wdecoster/nanopack] NanoPlot crash on openSUSE (#5) I believe this is a duplicate of wdecoster/NanoPlot#21<wdecoster/NanoPlot#21>, can you confirm? In my opinion this is a seaborn issue, and not NanoPlot itself. I will raise this on the seaborn github and see if they are willing to fix this, if not I shall fix it in NanoPlot. Cheers, Wouter — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#5 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ASb-WsGR7kaVGtZAeMW9-0SNWPM-RLcbks5tdDjygaJpZM4SlY-L>. This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.