Issue with bismark_genome_prep

[maf222]

Hello there I am running into an issue while running the human genome on the test file below. After I do the genome prep I see these messages. I verified that the bt2l files exist and when running ls -l there it seems quite normal but I am getting a very small methylation number 50 which seems wrong. I ran the same test file on a different machine a while back which may have had a different version of the reference genome but it did have the same (untrimmed) version of the test data file. On this PC the number for the methylation was over 4000 so it would seem odd that this is so different now. I don't currently have access to the old PC where I ran it before so it will be hard to verify if the versions of the reference genome are very different. I am wondering what the issue could be any help would be appreciated.
I ran the commands (genome prep and the alignment) without any sort of additional options.
test_data.txt

The Bowtie 2 index of the C->T converted genome seems to be faulty or non-existant ('BS_CT.1.bt2'). Please runthe bismark_genome_preparation before running Bismark
The Bowtie 2 index of the C->T converted genome seems to be faulty or non-existant ('BS_CT.2.bt2'). Please runthe bismark_genome_preparation before running Bismark
The Bowtie 2 index of the C->T converted genome seems to be faulty or non-existant ('BS_CT.3.bt2'). Please runthe bismark_genome_preparation before running Bismark
The Bowtie 2 index of the C->T converted genome seems to be faulty or non-existant ('BS_CT.4.bt2'). Please runthe bismark_genome_preparation before running Bismark
The Bowtie 2 index of the C->T converted genome seems to be faulty or non-existant ('BS_CT.rev.1.bt2'). Pleaserun the bismark_genome_preparation before running Bismark
The Bowtie 2 index of the C->T converted genome seems to be faulty or non-existant ('BS_CT.rev.2.bt2'). Pleaserun the bismark_genome_preparation before running Bismark
The Bowtie 2 index of the G->A converted genome seems to be faulty or non-existant ('BS_GA.1.bt2'). Please runbismark_genome_preparation before running Bismark
The Bowtie 2 index of the G->A converted genome seems to be faulty or non-existant ('BS_GA.2.bt2'). Please runbismark_genome_preparation before running Bismark
The Bowtie 2 index of the G->A converted genome seems to be faulty or non-existant ('BS_GA.3.bt2'). Please runbismark_genome_preparation before running Bismark
The Bowtie 2 index of the G->A converted genome seems to be faulty or non-existant ('BS_GA.4.bt2'). Please runbismark_genome_preparation before running Bismark
The Bowtie 2 index of the G->A converted genome seems to be faulty or non-existant ('BS_GA.rev.1.bt2'). Pleaserun bismark_genome_preparation before running Bismark
The Bowtie 2 index of the G->A converted genome seems to be faulty or non-existant ('BS_GA.rev.2.bt2'). Pleaserun bismark_genome_preparation before running Bismark

Couldn't find a traditional small Bowtie 2 index for the genome specified (ending in .bt2). Now searching for a large index instead (64-bit index ending in .bt2l)...
64-bit large genome Bowtie 2 index found...
FastQ format assumed (by default)

[maf222]

oh I had to change the test data to a txt to have it work for GitHub the one that was run is a fasq

[FelixKrueger]

Hmm, to be honest I have some difficulty extracting whether you do currently have a problem at all, and if so what it is...

Just generally, you fill need a .fa file (or several) for the genome preparation, and a .fastq file (of the .gz versions) for alignments. If you still encounter any issues, can you please link the exact commands and the relevant error messages? Thanks

[maf222]

It seems like maybe there is just a mismatch between my ref genome and my test data. When I ran the files on bismark/test_files on the GitHub my results seemed correct are these files a valid way to verify my setup?

[maf222]

Is there an answer key for the bismark/test_files so I can verify my setup?

[FelixKrueger]

Not sure I follow, but generally: if the tools are installed properly and the commands run to completion, it is typically a sign that your setup is functional. For anything more specific I would need more details (commands/output etc).

[maf222]

This is my output it looks correct to me but I am just worried about my setup so I just wanted to verify that this looks correct.

[FelixKrueger]

this looks just fine!