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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Failed to determine read length for library #0 for IonTorrent data #999

Open samche42 opened 2 years ago

samche42 commented 2 years ago

Description of bug

Hi! I'm a smidge baffled and can't find a solution online.

I'm trying to assemble five IonTorrent single read datasets. The read correction worked just fine and then when the assembly began in earnest, it quits with the following error:

"Failed to determine read length for library #0. Check that not only merged reads are present." What is library #0?

It also looks like library #4 may have all reads removed? I'm not sure if I'm reading the log file correctly though. What is extra baffling here is that that particular library assembled just fine on its own. Any suggestions on what I'm messing up and what to do?

Thanks :)

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes genome assembler v3.15.0

Operating System

Ubuntu 20.04.4 LTS (GNU/Linux 5.4.0-117-generic x86_64)

Python Version

Python 3.8.1

Method of SPAdes installation

manual

No errors reported in spades.log

asl commented 2 years ago

Hello.

Sorry, it seems that library are counted from 0 there. So, in this particular case these are libraries 1 and 5. What is the size of /media/bigdrive1/sam/Spirochete_Project/All_Spades_Assembly/corrected/003D_200bp_lib0_1.cor.fasta and /media/bigdrive1/sam/Spirochete_Project/All_Spades_Assembly/corrected/003B_200bp_lib4_1.cor.fasta?

samche42 commented 2 years ago

Each appear to be only 48 bytes :|

asl commented 2 years ago

And what is inside?

samche42 commented 2 years ago

Absolutely nothing. Empty files.

asl commented 2 years ago

Well, it may happen that one library could cause others to appear completely "bad", but still this is something pretty unexpected. IonTorrent handling code did not change over last 5-6 years. So, as a workaround I'd suggest to perform separate error correction and them provide all these files adding --only-assembler.

samche42 commented 2 years ago

Ya -I've been assembling IonTorrent data quite happily with Spades for years! Big fan :) Will give your suggestion a bash! Thank you!