bowtie2 error "Read xyz has more quality values than read characters" -> signal 6 (ABRT)

Question

[normanreppingen]

Hi,

i used bowtie2 without problems on many files which worked great, now it gives the error message: "Read xyz has more quality values than read characters" I re - downloaded the fastq file, same problem.

head SRR1191170_NF.fastq

gives the following:

@SRR1191170.1 1/1
T012122020210210110200211200001113113312113321..331
+
!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ338&5554
@SRR1191170.2 2/1
T01212202021021011020021120000111311331211332133331
+
!JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ32913444
@SRR1191170.3 3/1
T30122212022122110022001201102011112320012302211120

The url of the file was: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR119/000/SRR1191170/SRR1191170_2.fastq.gz

What can i do to make this file more digestible for bowtie2?

I tried to install fqtools with bioconda to see if there is an option to remedy this, but starting the fqtools also left me with an error message.

I currently do not know how to compile / install it manually on mac.

dyld: Library not loaded: @rpath/libdeflate.so
  Referenced from: /Users/normanreppingen/anaconda3/lib/libhts.1.9.dylib
  Reason: image not found
Abort trap: 6

I need to know what these cancer associated fibroblasts are doing, but i am facing challenges...

Is there a helpful parameter for bowtie2 which i do not know?

Best regards,

Norman

P.S.: I bought the Biostar Handbook recently, and read carefully about bowtie2 - but this error really seems to be an exception.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Answer 1

[microfuge]

The SRA ID seems to be from ABI Solid technology https://www.ncbi.nlm.nih.gov/sra/?term=SRR1191170

[ATpoint]

From manual: Bowtie 2 does not align colorspace reads. Nothing you can do about it. You can try bowtie1 but you will need to download the respective genome index for color-space reads.

[normanreppingen]

Dear ATpoint, that was very quick! So i would have messed in vain... I have a mm9 mouse genome somewhere, i will try this. Thank you very much!

Best regards,

Norman

(who also dislikes western blots a lot)

[ATpoint]

There are premade indices for SOLiD on the bowtie website. +1 for disliking WBs :)