error: [fai_fetch_seq] The sequence "chr1_CT_converted" not found about methyldackel HOT 8 CLOSED

What does samtools view -H your_file.bam | grep chr1_CT_converted show? What about grep chr1_CT_converted your_fasta_file?

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samtools view -H MUP_merged_sorted.bam | grep chr1_CT_converted
@sq SN:chr1_CT_converted LN:197195432

grep chr1_CT_converted mm9.fa
#returns nothing

(as a side note: the reference genome is within the same folder as the output of bismark_genome_preparation with the CT_conversion.fa and GA_conversion.fa files. Even when I use the conversion fasta files, I get the same error)

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It looks like you're using an intermediate file created by bismark rather than what should be the final one. The final BAM file should contain chromosome names like chr1 and chr2.

from methyldackel.

thank you for pointing that out. I will go ahead and double check that.
Thank you for your time and help!

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I got a similar warning:

faidx_fetch_seq returned -2 while trying to fetch the sequence for tid chr1:999998-2000000!
Note that the output will be truncated!
[E::faidx_adjust_position] The sequence "chr1" not found

fasta and bam:

samtools view -H my.sorted.bam | grep "chr1"
@SQ     SN:chr1 LN:248956422
@SQ     SN:chr10        LN:133797422
@SQ     SN:chr11        LN:135086622
@SQ     SN:chr12        LN:133275309

cat GRCh38.primary_assembly.genome.fa | grep ">" 
>chr1 1
>chr2 2
>chr3 3

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If you look through the .fai file, is there a chr1 entry?

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cat GRCh38.primary_assembly.genome.fa.fa
i | grep chr1
chr1    248956422       8       60      61
chr10   133797422       1702798442      60      61
chr11   135086622       1838825832      60      61
chr12   133275309       1976163908      60      61
chr13   114364328       2111660483      60      61

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Odd, try recreating the fasta index, maybe that will help.

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