Could not locate a Bowtie index corresponding to basename

Question

[Rahul]

Dear all, Can some one suggest me how to correct this problem. I am running wsl based Oligominer tool for probe designing. Th ecommand after Bowtie2 build was like this. But i experienced the error 'Could not locate a Bowtie index corresponding to basename' and sometimes other errors like 'bowtie2-align exited with value 1'. how to rectify these errors and run the Oligominer smoothly.

(ol) rahul@DESKTOP-J3Q9JD9:~/ol_dir/OligoMiner$ bowtie2 -x/Users/Rahul/AppData/Local/Packages/CanonicalGroupLimited.Ubuntu_79rhkp1fndgsc/LocalState/rootfs/home/rahul/ol_dir/OligoMiner/sequence_1 -U sequence_1.fastq --no-hd -t -k 100 --very-sensitive-local -S sequence_1_u.sam

Thanks

[GenoMax]

bowtie2 -x/Users/Rahul/

Not certain but it looks like you are missing a space between x and rest of the path. It should be

bowtie2 -x /Users/Rahul/

[Rahul]

Thank for you reply. I tried with space after bowtie2 -x /Users/Rahul/..... But sam errors is still coming.

can you suggest some more tips

Thanks

[GenoMax]

Is this path correct?

/Users/Rahul/AppData/Local/Packages/CanonicalGroupLimited.Ubuntu_79rhkp1fndgsc/LocalState/rootfs/home/rahul/ol_dir/OligoMiner/sequence_1

and if it is can you show the output of

ls -l /Users/Rahul/AppData/Local/Packages/CanonicalGroupLimited.Ubuntu_79rhkp1fndgsc/LocalState/rootfs/home/rahul/ol_dir/OligoMiner/sequence_1*

Did you create the bowtie2 index or is this something Oligominer does internally?

[Rahul]

this command is not getting detected but the folder in which the files are saved are like:

(ol) rahul@DESKTOP-J3Q9JD9:~/ol_dir/OligoMiner$ ls
ExampleFiles                             environment.yml       ncbi-genomes-2022-11-05  sequence_1.fasta
GCF_001051385.1_ASM105138v1_genomic.fna  fastqToBed.py         output.sam               sequence_1.fastq
GCF_001051385.fastq                      genomes.fna           outputClean.py           sequence_1.rev.1.bt2
ImageQuantification                      index_name.1.bt2      probeRC.py               sequence_1.rev.2.bt2
LICENSE                                  index_name.2.bt2      probeTm.py               sequence_1_u.sam
README.md                                index_name.3.bt2      sal_t                    sequence_1_u_probes.bed
bedChainer.py                            index_name.4.bt2      sequence_1.1.bt2         structureCheck.py
bedToFastq.py                            index_name.rev.1.bt2  sequence_1.2.bt2
blockParse.py                            index_name.rev.2.bt2  sequence_1.3.bt2
citation.bib                             kmerFilter.py         sequence_1.4.bt2

[Rahul]

when i search fastq file. this file is found in this path: Users/Rahul/AppData/Local/Packages/CanonicalGroupLimited.Ubuntu_79rhk p1fndgsc/LocalState/rootfs/home/rahul/ol_dir/OligoMiner/sequence_1

altough i have copied the data of Oligominer folder to downloads section also. Can wsl take commands from downloads section also?

[Rahul]

Did you create the bowtie2 index or is this something Oligominer does internally?

I think Oligominer did it internally

My previous command was : (ol) rahul@DESKTOP-J3Q9JD9:~/ol_dir/OligoMiner$ bowtie2-build sequence_1.fasta sequence_1

[Rahul]

GenoMax please suggest Python learning tool/literature for wsl based programming where ican learn about commands and modifications.

Thanka & regards

[GenoMax]

https://python.swaroopch.com/ is a good resource.

It is not going to be simply about learning commands when you are trying to learn a new programming language.

[Rahul]

Can someone suggest to me how (any software or online approach) to join the approx 71 contigs of the bacterial genome into one FASTA file of the genome in the correct order. I have a reference genome of the same bacterial species but a different strain Can we choose it as a reference genome?

[GenoMax]

Please do not ask unrelated questions in an existing thread. This question should have been posted in a new thread. But before doing that always search the forum using google.

These past threads may be useful:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121819/
reference-guided denovo assembly

Answer 1

[GenoMax]

Based on the information you included the command you should try (assuming you are in ~/ol_dir/OligoMiner directory) :

bowtie2 -x ~/ol_dir/OligoMiner/sequence_1 -U sequence_1.fastq --no-hd -t -k 100 --very-sensitive-local -S sequence_1_u.sam

I already see a sequence_1_u.sam file there. So be careful about this process. You could overwrite files and lose data if you are not comfortable using the command line.

[Rahul]

Thank You so much. The command you suggested worked.

Next I gave another command for cleaning of probes but it got interruptions. Pls have a look :

(ol) rahul@DESKTOP-J3Q9JD9:~/ol_dir/OligoMiner$ python outputClean.py -u -f sequence_1_u.sam
Traceback (most recent call last):
  File "outputClean.py", line 486, in <module>
    main()
  File "outputClean.py", line 480, in main
    reportVal, debugVal, metaVal, outNameVal, startTime)
  File "outputClean.py", line 70, in cleanOutput
    if x[0] is not '@' else ' ' for x in file_read]
IndexError: list index out of range

How should I proceed. Is there any key thing left in the command? Please rectify me

[Rahul]

hi I tried another command also like this but few errors are coming up. Please suggest me what kind of command error are there in these commands:

(ol) rahul@DESKTOP-J3Q9JD9:~/ol_dir/OligoMiner$ python kmerFilter.py -f sequence_1_u_probes.bed -m 18 -j sequence_1.jk -k 4
Failed to parse header of file 'sequence_1.jk'
Traceback (most recent call last):
  File "kmerFilter.py", line 324, in <module>
    main()
  File "kmerFilter.py", line 318, in main
    reportVal, debugVal, metaVal, startTime)
  File "kmerFilter.py", line 186, in runFilter
    % (cleanNum, candsNum, float(cleanNum)/float(candsNum) * 100,
ZeroDivisionError: float division by zero

[Rahul]

GenoMax pls suggest some tricks of you know GenoMax

[GenoMax]

No tricks can be employed when analyzing data. You will have to check and make sure you are using the correct command line. Also make sure that you are using correct version of python that the program needs (v.2.x and 3.x are very different).

Most important thing is check outputs at every step of the process. Just because a command ran does not mean it produced correct/usable result. You need to verify that result files actually make sense before you go to the next step.