Bowtie 2 index files exist but return Error: Could not find Bowtie 2 index files (humanGRCh38.*.bt2l)
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2.3 years ago
skurkure • 0

As I have stated above, I have received an error in running tophat, with the output below. The command I supplied was tophat humanGRCh38 gerald_C2DBEACXX_3.fq,gerald_C1TD1ACXX_8_ACAGTG.fq , as I was running tophat from the directory in which the bt2l files were installed. I have supplied the prefix as well, but it did not work. I have gotten the same error when I supply the entire present working directory and the prefix, I got the same problem. Anyone else run into this, and if yes how did you fix it? I know that the version of bowtie that I am using is correct because the files are in the correct format.

$ls gerald_C1TD1ACXX_8_ACAGTG.bam Homo_sapiens.GRCh38.96.gtf humanGRCh38.3.bt2l gerald_C1TD1ACXX_8_ACAGTG.fq Homo_sapiens.GRCh38.dna.toplevel.fa humanGRCh38.4.bt2l gerald_C2DBEACXX_3.bam humanGRCh38.1.bt2l tophat_out gerald_C2DBEACXX_3.fq humanGRCh38.2.bt2l$ tophat humanGRCh38 gerald_C2DBEACXX_3.fq,gerald_C1TD1ACXX_8_ACAGTG.fq

[2019-07-02 08:34:27] Beginning TopHat run (v2.1.1)

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[2019-07-02 08:34:27] Checking for Bowtie

Bowtie version: 2.3.4.1

[2019-07-02 08:34:27] Checking for Bowtie index files (genome)..

Error: Could not find Bowtie 2 index files (humanGRCh38.*.bt2l)

 RNA-Seq Tophat Bowtie2 Index • 1.1k views ADD COMMENT 0 Entering edit mode Did you make this index yourself? Has it been tested before this? What do you get if you do: bowtie2-inspect -n humanGRCh38  You should see the names of chromosomes being listed like this (truncated, may not look exactly like this, we are testing to make sure you don't get an error). chr1 AC:CM000663.2 gi:568336023 LN:248956422 rl:Chromosome M5:6aef897c3d6ff0c78aff06ac189178dd AS:GRCh38 chr2 AC:CM000664.2 gi:568336022 LN:242193529 rl:Chromosome M5:f98db672eb0993dcfdabafe2a882905c AS:GRCh38 chr3 AC:CM000665.2 gi:568336021 LN:198295559 rl:Chromosome M5:76635a41ea913a405ded820447d067b0 AS:GRCh38 chr4 AC:CM000666.2 gi:568336020 LN:190214555 rl:Chromosome M5:3210fecf1eb92d5489da4346b3fddc6e AS:GRCh38  ADD REPLY 0 Entering edit mode No, I did not build this index myself. I used a pre-built index from ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.tar.gz When I do bowtie2-inspect -n humanGRCh38 I get an error  bowtie2-inspect -n humanGRCh38
bowtie2-inspect-l: word_io.h:125: T readU(FILE*, bool) [with T = long unsigned int; FILE = _IO_FILE]: Assertion false' failed.

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I see the following files in the tar archive you linked above. So it looks like you did not get the full set of files or uncompressing went wrong somewhere.

\$ tar -tvf GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.tar.gz
-rw-r--r-- kitts/gassmbly 982525150 2014-11-18 17:09 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.1.bt2
-rw-r--r-- kitts/gassmbly 733719120 2014-11-18 17:09 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.2.bt2
-rw-r--r-- kitts/gassmbly     10880 2014-11-18 16:01 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.3.bt2
-rw-r--r-- kitts/gassmbly 733719113 2014-11-18 16:01 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.4.bt2
-rw-r--r-- kitts/gassmbly 982525150 2014-11-18 18:16 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.rev.1.bt2
-rw-r--r-- kitts/gassmbly 733719120 2014-11-18 18:16 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.rev.2.bt2

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Unless absolutely essential you may want consider using a current RNAseq splice aware aligner like STAR, bbmap instead of TopHat`.