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--- phylogeny_protocol6 [2022/02/08 14:03] – 134.190.232.106
+++ phylogeny_protocol6 [2022/02/24 10:23] (current) – 38.20.199.40
@@ Line 97: / Line 97: @@
 /misc/scratch2/xizhang/PhyloTol/Scripts
 FileNotFoundError: [Errno 2] No such file or directory: '/Users/katzlab32/Documents/PhyloTOL/DataFiles//duplication'
 pipeline_parameter_file.txt
 </code>
+**Downloading, trimming, assembly**
+Errors 1:MultiFastQC
+<code>
+   MultiFastQC.py
+os.system('fastqc ' + file + ' --outdir=' + pathOutdir)
+		#pathFQC + "/Contents/MacOS/fastqc"
+</code>
+Errors 2: BBmap
+<code>
+TransPipe2.py
+_R1 to _1
+_R2 to _2
+</code>
+Errors 3: BBmap2
+<code>
+python2 TransPipe2.py parameter.txt your email  (Email doesnot matter, must be python2)
+parameter.txt (must be careful with the \n, in MacOS which is \r\n)
+</code>
+Errors 4: PLT1 = Post assembly pipeline
+<code>
+wrapper.py
+'_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>
+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
+_FilterPartials.py
+	### Update values and names if you have used an alternative Database of Proteins!
+Error:
+_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>