Run failure

[Concha Eloko Robby]

Bonjour !

I tried running the script on a recently sequenced phage. The input are paired reads, the command line is as follow :

/home/user/software/phageterm-1.0.12/PhageTerm.py -f K10PH82C1_S15_R1_001.fastq  -p K10PH82C1_S15_R2_001.fastq -r K10PH82C1_sequence.fasta -n K10PH82C1 -t installation_test -c 4

After calculating coverage values until 100%, I get the following error message :

AttributeError: 'module' object has no attribute 'VERSION'
identity=[ImageReader@0x7f6515c8c8d0

I tried running the script with the test data as follow :

/home/user/software/phageterm-1.0.12/PhageTerm.py -f Mu-like_R1.fastq -p Mu-like_R2.fastq -r Mu-like.fasta

but I get the same error.

if Image.VERSION.startswith('1.1.7'): im.load()
AttributeError: 'module' object has no attribute 'VERSION'
identity=[ImageReader@0x7f76dd4ac550]

Is there a way this can be fixed ?

Best,
Robby

[Julian Garneau]

Bonsoir :)

When you run the installation test, could try without your own reads, as follow :

$ /home/user/software/phageterm-1.0.12/PhageTerm.py -t C5

Tell me if this command works properly on your system. If not, maybe you should force launching phageterm with python2 :

$ python2 PhageTerm.py -t C5

And with your own reads :

$ python2 PhageTerm.py -f K10PH82C1_S15_R1_001.fastq -p K10PH82C1_S15_R2_001.fastq -r K10PH82C1_sequence.fasta -n K10PH82C1 -c 4

Keep me posted if it worked with one of those ways to run the software.

Good luck

P.S. Do you expect your phage to be a Mu-like phage?

[Concha Eloko Robby]

Hi again,

Thanks for your quick answer. Before receiving it, I tried using the Maximilian Press 's version compatible with python3. The process went until the end, i.e without any error messages but I reckon some of the outputs were incorrect : the corrected fasta was empty for all the tested phages (~70). However, I got some seemingly good reports : I compared one of them with one obtained on the galaxy platform of the institute and they were identical. However I am still very interested in the corrected sequence.

After reading you reply I tried, as you recommended me, and I got the same error message. Nevertheless, I got for some phages a corrected fasta sequence without reports. (Seems congruent with the following error message) :

Calculating coverage values, please wait (may take a while)...

100.0 %

Finished calculating coverage values, the remainder should be completed rapidly

Traceback (most recent call last):
  File "/home/user/software/phageterm-1.0.12/PhageTerm.py", line 426, in <module>
    CreateReport(phagename, seed, added_whole_coverage, draw, Redundant, P_left, P_right, Permuted, P_orient, termini_coverage_norm_close, picMaxPlus_norm_close, picMaxMinus_norm_close, gen_len, tot_reads, P_seqcoh, phage_plus_norm, phage_minus_norm, ArtPackmode, termini, forward, reverse, ArtOrient, ArtcohesiveSeq, termini_coverage_close, picMaxPlus_close, picMaxMinus_close, picOUT_norm_forw, picOUT_norm_rev, picOUT_forw, picOUT_rev, lost_perc, ave_whole_cov, R1, R2, R3, host, host_len, host_whole_coverage, picMaxPlus_host, picMaxMinus_host, surrounding, drop_cov, paired, insert, phage_hybrid_coverage, host_hybrid_coverage, added_paired_whole_coverage, Mu_like, test_run, P_class, P_type, P_concat)
  File "/home/user/software/phageterm-1.0.12/_modules/functions_PhageTerm.py", line 1815, in CreateReport
    doc.build(report)
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/platypus/doctemplate.py", line 1213, in build
    BaseDocTemplate.build(self,flowables, canvasmaker=canvasmaker)
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/platypus/doctemplate.py", line 969, in build
    self.handle_flowable(flowables)
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/platypus/doctemplate.py", line 834, in handle_flowable
    if frame.add(f, canv, trySplit=self.allowSplitting):
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/platypus/frames.py", line 196, in _add
    flowable.drawOn(canv, self._x + self._leftExtraIndent, y, _sW=aW-w)
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/platypus/flowables.py", line 111, in drawOn
    self._drawOn(canvas)
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/platypus/flowables.py", line 92, in _drawOn
    self.draw()#this is the bit you overload
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/platypus/tables.py", line 1425, in draw
    self._drawCell(cellval, cellstyle, (colpos, rowpos), (colwidth, rowheight))
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/platypus/tables.py", line 1558, in _drawCell
    v.drawOn(self.canv,x,y)
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/platypus/flowables.py", line 111, in drawOn
    self._drawOn(canvas)
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/platypus/flowables.py", line 92, in _drawOn
    self.draw()#this is the bit you overload
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/platypus/flowables.py", line 516, in draw
    mask=self._mask,
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/pdfgen/canvas.py", line 924, in drawImage
    rawdata = image.getRGBData()
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/lib/utils.py", line 886, in getRGBData
    annotateException('\nidentity=%s'%self.identity())
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/lib/utils.py", line 1390, in annotateException
    rl_reraise(t,v,b)
  File "/home/user/.local/lib/python2.7/site-packages/reportlab/lib/utils.py", line 871, in getRGBData
    if Image.VERSION.startswith('1.1.7'): im.load()
AttributeError: 'module' object has no attribute 'VERSION'
identity=[ImageReader@0x7fe16eaa7450]

I guess I could combine the output from those 2 different sources.

Thanks for your help and congrats for the work done.

Ps : I actually had no expectation regarding the phage packaging mechanism.

[Julian Garneau]

Hi again Concha,

Could you send me an e-mail at julian.garneau@pasteur.fr

WIll be easier to exchange on there,

Thanks!