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phylogeny_protocol6

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phylogeny_protocol6 [2022/02/15 17:49] – 38.20.199.40phylogeny_protocol6 [2022/02/24 10:23] (current) – 38.20.199.40
Line 138: Line 138:
 wrapper.py wrapper.py
 '_rnaSPAdes --minLen 200 --spades '_rnaSPAdes --minLen 200 --spades
 +
 +
 +---Fatal error---
 +Empty file ../Sr_di_Espc/Sr_di_Espc_WTA_NBU.Renamed_tga_ORF.aa.fasta
 +
 +
 +/opt/perun/bin/usearch -ublast ../Sr_di_Espc/Sr_di_Espc_WTA_NBU.Renamed_taa_ORF.aa.fasta -db ../../Databases/db_StopFreq/RepEukProts.udb -evalue 1e-5 -maxaccepts 1 -blast6out ../Sr_di_Espc/Sr_di_Espc_WTA_NBU.Renamed_taa_ORF.RepEukProts.tsv
 +
 +---Fatal error---
 +Empty file ../Sr_di_Espc/Sr_di_Espc_WTA_NBU.Renamed_taa_ORF.aa.fasta
 +Traceback (most recent call last):
 +  File "4_InFrameStopFreq.py", line 745, in <module>
 +    main()
 +  File "4_InFrameStopFreq.py", line 739, in main
 +    hunt_for_stops(args)
 +  File "4_InFrameStopFreq.py", line 686, in hunt_for_stops
 +    +'\t'+"%.2f" % ((float(taa_inframe)*1000)/float(total_codons))+'\n')
 +ZeroDivisionError: float division by zero
 </code> </code>
 +
 +
 +<code>
 +wrapper.py fifth step
 +
 +/usr/lib/python2.7/dist-packages/Bio/Seq.py:2309: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.
 +  BiopythonWarning)
 +</code>
 +
 +Errors 4: PLT1 = Post assembly pipeline 
 +
 +<code>
 +#step sixth
 +6_FilterPartials.py
 + ### Update values and names if you have used an alternative Database of Proteins!
 +
 +Error:
 +6_FilterPartials.py
 +
 + 
 +This OG group ‘OG5_141800’ cannot be found in the dictionary ‘OGLenDB’ in 6_FilterPartials.py:
 +
 + 
 +Question:
 +How to add new OG to this list? (how can we get the length info of each OG?)
 +
 +</code>
 +
 +Errors 5:
 +<code>
 +Failed to determine offset! Specify it manually and restart, please!
 +Try setting --phred-offset 33 or 64 manually and re-run. If you have recent sequence data then the offset will be 33 for sure.
 +
 +How much RAM are you allocating to this job. Appears to be 250GB.
 +</code>
 +
  
 <Last updated by Xi Zhang on Feb 8th,2022> <Last updated by Xi Zhang on Feb 8th,2022>
phylogeny_protocol6.1644961793.txt.gz · Last modified: by 38.20.199.40