Hi,
I am using the following call to spray-and-pray.py:
spray-and-pray.py -t 20 --euk --meta --spades -bam ${prefix}.pairedReads2assembly.sorted.bam -g $file -ref /home/liam/data/nr/nr.dmnd -out spraynpray_out/$bin
I am receiving the following error. The number "1.00425e+06" is the same across all of my datasets, so I assume that is internal to spray and pray, and not a function of my data?
Running Prodigal: calling ORFs from provided contigs
Running Diamond BLAST
Extracting coverage information from the provided BAM files
Calculating GC-content
Preparing summary: spraynpray_out/rubra.4.csv
Traceback (most recent call last):
File "/home/liam/tools/SprayNPray/spray-and-pray.py", line 779, in <module>
depthDict[ls[0]]["length"] = int(ls[1])
ValueError: invalid literal for int() with base 10: '1.00425e+06'
This is inside a for loop that is printing $bin, $prefix, and $file each iteration, so I am sure those are assigned correctly.
The files that are being generated are:
*-cds.ffn (which has the variable $file as its prefix instead of what follows the -out flag)
*-proteins.faa (which has the variable $file as its prefix instead of what follows the -out flag)
*.blast (which has the variable $file as its prefix instead of what follows the -out flag)
*-top100.csv
I think there is supposed to be at least one other file? Which I assume is the "preparing summary" output that is being blocked by that error?
Hi,
I am using the following call to spray-and-pray.py:
spray-and-pray.py -t 20 --euk --meta --spades -bam ${prefix}.pairedReads2assembly.sorted.bam -g $file -ref /home/liam/data/nr/nr.dmnd -out spraynpray_out/$binI am receiving the following error. The number "1.00425e+06" is the same across all of my datasets, so I assume that is internal to spray and pray, and not a function of my data?
This is inside a for loop that is printing $bin, $prefix, and $file each iteration, so I am sure those are assigned correctly.
The files that are being generated are:
*-cds.ffn (which has the variable $file as its prefix instead of what follows the -out flag)
*-proteins.faa (which has the variable $file as its prefix instead of what follows the -out flag)
*.blast (which has the variable $file as its prefix instead of what follows the -out flag)
*-top100.csv
I think there is supposed to be at least one other file? Which I assume is the "preparing summary" output that is being blocked by that error?