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harvardinformatics / TranscriptomeAssemblyTools

A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.
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error message #2

Closed gdamasco closed 4 years ago

gdamasco commented 5 years ago

Dear Adam,

I am trying to use RemoveFastqcOverrepSequenceReads.py and I am getting the following error message. Could you please save me?

python /home/cavender/gdamasco/bin/TranscriptomeAssemblyTools/RemoveFastqcOverrepSequenceReads.py -1 unfixrm_G_11_S4_R1_001.cor_val_1.fq -2 unfixrm_G_11_S4_R2_001.cor_val_2.fq Traceback (most recent call last): File "/home/cavender/gdamasco/bin/TranscriptomeAssemblyTools/RemoveFastqcOverrepSequenceReads.py", line 46, in leftseqs=ParseFastqcLog(opts.l_fastqc) File "/home/cavender/gdamasco/bin/TranscriptomeAssemblyTools/RemoveFastqcOverrepSequenceReads.py", line 33, in ParseFastqcLog with open(fastqclog) as fp: TypeError: coercing to Unicode: need string or buffer, NoneType found

sraj214 commented 4 years ago

Dear Adam,

I am trying to use RemoveFastqcOverrepSequenceReads.py and I am getting the following error message. Could you please save me?

python /home/cavender/gdamasco/bin/TranscriptomeAssemblyTools/RemoveFastqcOverrepSequenceReads.py -1 unfixrm_G_11_S4_R1_001.cor_val_1.fq -2 unfixrm_G_11_S4_R2_001.cor_val_2.fq Traceback (most recent call last): File "/home/cavender/gdamasco/bin/TranscriptomeAssemblyTools/RemoveFastqcOverrepSequenceReads.py", line 46, in leftseqs=ParseFastqcLog(opts.l_fastqc) File "/home/cavender/gdamasco/bin/TranscriptomeAssemblyTools/RemoveFastqcOverrepSequenceReads.py", line 33, in ParseFastqcLog with open(fastqclog) as fp: TypeError: coercing to Unicode: need string or buffer, NoneType found

Did you solve this issue ? I am new to bioinfomatics and have been following the same pipeline for Denovo-sequencing and I have the exact error as yours while running this script.

adamfreedman commented 4 years ago

as best as i can tell, you never provided as arguments (via -fql and -fqr) the text files output by fastqc. that is whether the over-represented sequences come from. sorry for the very late reply to this. working on updating this script today ... so stay tuned for a new version