timbalam
commented
8 years ago Hi maria-456,
Thanks for the report!
I'm currently working on a new version of GroopM. As this is my focus, I probably won't get around to fixing bugs such as this one in the current version that aren't relevant to the new version.
The new version I think will be much better. I will let you know when it is ready.
Cheers, Tim
On 28/05/2016 3:58 PM, maria-456 wrote:
Hello, I have downloaded GroopM and keep getting this error when I get to the groopm core step. I have tried re-mapping and recreating my bam files as well as reinstalling groopm and it's dependencies, but I still keep getting this error and can't figure out why!
`*** [[GroopM 0.3.4]] Running in core creation mode...
Loading data from: groopm10.db GroopM DB version (5) up to date Loaded indices with condition: length >= 1500 Working with: 13327 contigs Loading coverage profiles Loading PCA kmer sigs (10 dimensional space) Loading PCA kmer variance (total variance: 0.81) Loading contig names Loading contig lengths (Total: 90577575 BP) Loading contig GC ratios (Average GC: 0.488) Creating color map { THIS: 0:00:08.394 || TOTAL: 0:00:08.406 } Loading transformed data Reticulating splines { THIS: 0:00:01.369 || TOTAL: 0:00:09.775 } Create cores Unexpected error: Traceback (most recent call last): File "/media/acclomator/egraham/.local/bin/groopm", line 381, in GM_parser.parseOptions(args) File "/media/acclomator/egraham/.local/lib/python2.7/site-packages/groopm/groopm.py", line 138, in parseOptions gf=gf) File "/media/acclomator/egraham/.local/lib/python2.7/site-packages/groopm/cluster.py", line 208, in makeCores self.initialiseCores(kmerThreshold, coverageThreshold) File "/media/acclomator/egraham/.local/lib/python2.7/site-packages/groopm/cluster.py", line 231, in initialiseCores self.populateImageMaps() File "/media/acclomator/egraham/.local/lib/python2.7/site-packages/groopm/cluster.py", line 914, in populateImageMaps self.incrementViaRowIndex(row_index, p) File "/media/acclomator/egraham/.local/lib/python2.7/site-packages/groopm/cluster.py", line 921, in incrementViaRowIndex self.incrementAboutPoint(0, point[0], point[1], multiplier=multiplier) File "/media/acclomator/egraham/.local/lib/python2.7/site-packages/groopm/cluster.py", line 952, in incrementAboutPoint self.imageMaps[view_index,px-1,py-1] += valC # Top left corner IndexError: only integers, slices (|:|), ellipsis (|...|), numpy.newaxis (|None|) and integer or boolean arrays are valid indices `
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maria-456
Hello, I have downloaded GroopM and keep getting this error when I get to the groopm core step. I have tried re-mapping and recreating my bam files as well as reinstalling groopm and it's dependencies, but I still keep getting this error and can't figure out why!
`*** [[GroopM 0.3.4]] Running in core creation mode...
Loading data from: groopm10.db GroopM DB version (5) up to date Loaded indices with condition: length >= 1500 Working with: 13327 contigs Loading coverage profiles Loading PCA kmer sigs (10 dimensional space) Loading PCA kmer variance (total variance: 0.81) Loading contig names Loading contig lengths (Total: 90577575 BP) Loading contig GC ratios (Average GC: 0.488) Creating color map { THIS: 0:00:08.394 || TOTAL: 0:00:08.406 } Loading transformed data Reticulating splines { THIS: 0:00:01.369 || TOTAL: 0:00:09.775 } Create cores Unexpected error: <type 'exceptions.IndexError'> Traceback (most recent call last): File "/media/orlandor/ella/.local/bin/groopm", line 381, in
GM_parser.parseOptions(args)
File "/media/orlando/ella/.local/lib/python2.7/site-packages/groopm/groopm.py", line 138, in parseOptions
gf=gf)
File "/media/orlandor/ella/.local/lib/python2.7/site-packages/groopm/cluster.py", line 208, in makeCores
self.initialiseCores(kmerThreshold, coverageThreshold)
File "/media/orlandor/ella/.local/lib/python2.7/site-packages/groopm/cluster.py", line 231, in initialiseCores
self.populateImageMaps()
File "/media/orlandor/ella/.local/lib/python2.7/site-packages/groopm/cluster.py", line 914, in populateImageMaps
self.incrementViaRowIndex(row_index, p)
File "/media/orlando/ella/.local/lib/python2.7/site-packages/groopm/cluster.py", line 921, in incrementViaRowIndex
self.incrementAboutPoint(0, point[0], point[1], multiplier=multiplier)
File "/media/orlando/ella/.local/lib/python2.7/site-packages/groopm/cluster.py", line 952, in incrementAboutPoint
self.imageMaps[view_index,px-1,py-1] += valC # Top left corner
IndexError: only integers, slices (
:), ellipsis (...), numpy.newaxis (None) and integer or boolean arrays are valid indices `