conda installed NanoPlot crashing

[michaelbroe]

NanoPlot is crashing on my latest data file. I have run this before successfully, but this is a new installation against a fresh installation of miniconda3.

fastq file is 237M.

Log file follows.

2018-01-16 14:45:24,368 NanoPlot 1.2.2 started with arguments Namespace(alength=False, bam=None, barcoded=False, color='#4CB391', downsample=None, drop_outliers=False, fastq=['fastq_runid_21b7fb54589a62a4e512bee4fc22daaa2cbaffc4.fastq'], fastq_minimal=None, fastq_rich=None, format='png', listcolors=False, loglength=False, maxlength=None, minqual=None, no_N50=False, outdir='NanoPlot', pickle=None, plots=['kde', 'pauvre'], prefix='', readtype='1D', report=False, store=False, summary=None, threads=16, verbose=False) 2018-01-16 14:45:24,368 Python version is: 3.6.2 |Continuum Analytics, Inc.| (default, Jul 20 2017, 13:51:32) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] 2018-01-16 14:45:24,392 Nanoplotter: valid output format png 2018-01-16 14:45:24,408 Nanoget: Starting to collect statistics from plain fastq file. 2018-01-16 14:46:03,116 Nanoget: Gathered all metrics of 11091 reads 2018-01-16 14:46:03,118 string indices must be integers Traceback (most recent call last): File "/mnt/data/broe.1/local/miniconda3/lib/python3.6/site-packages/nanoplot/NanoPlot.py", line 60, in main nanomath.write_stats(datadf, settings["path"] + "NanoStats.txt") File "/mnt/data/broe.1/local/miniconda3/lib/python3.6/site-packages/nanomath/nanomath.py", line 121, in write_stats stats = [Stats(df) for df in datadfs] File "/mnt/data/broe.1/local/miniconda3/lib/python3.6/site-packages/nanomath/nanomath.py", line 121, in <listcomp> stats = [Stats(df) for df in datadfs] File "/mnt/data/broe.1/local/miniconda3/lib/python3.6/site-packages/nanomath/nanomath.py", line 30, in __init__ self.number_of_bases = np.sum(df["lengths"]) TypeError: string indices must be integers

Cheers!

[wdecoster]

Hi,

That looks like a version incompatibility between the nanomath submodule and NanoPlot itself. Could you let me know which version of nanomath you have installed using

python -c "import nanomath ; print(nanomath.__version__)"

Looks like the most recent nanomath version (0.16.2) was recently added to bioconda

Cheers,
Wouter

[michaelbroe]

That's it:

$ python -c "import nanomath ; print(nanomath.__version__)" 0.16.2

[wdecoster]

Oh, what about NanoPlot itself then? For that you can use:

NanoPlot -v

[michaelbroe]

$ NanoPlot -v NanoPlot 1.2.2

[wdecoster]

Looks like the NanoPlot itself is outdated but update through bioconda is ongoing (see https://github.com/bioconda/bioconda-recipes/pull/7274)

The pip NanoPlot is at 1.8.1. I'll ask the bioconda team for help :)

[michaelbroe]

Uninstalled conda version, installed pip version against existing conda packages: all good. Thanks! Be nice to get conda version updated though...

[wdecoster]

Yes absolutely. Essentially, the build recipe for the new version is created, but since it has to go through automatic testing at Travis CI (which is currently very very slow) the latest version of NanoPlot (and NanoComp) are held back. Nanomath already got updated, but is now out of sync.

Please let me know if you encounter issues or have suggestions/feature requests!

[wdecoster]

(Bio)conda NanoPlot should be back in sync, with thanks to @druvus !

[michaelbroe]

Good stuff! If bioconda were always bleeding edge it would be perfect :)

Thanks, Michael

On Jan 18, 2018, 3:07 AM -0500, Wouter De Coster notifications@github.com, wrote:

(Bio)conda NanoPlot should be back in sync, with thanks to @druvushttps://github.com/druvus !

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/wdecoster/NanoPlot/issues/41#issuecomment-358568844, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ABn-wYQq72TzdXwmE9a2RV9AeQqc1ssCks5tLvu6gaJpZM4RgV-w.