NanoPlot crash on openSUSE

[gwaldbieser]

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

[wdecoster]

I believe this is a duplicate of https://github.com/wdecoster/NanoPlot/issues/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

[gwaldbieser]

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#21https://github.com/wdecoster/NanoPlot/issues/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

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