BWA error: fail to locate the index files

[Gig77]

I am getting the following error with abra v0.77:

Thu Jun 12 19:48:43 CEST 2014 : Aligning contigs Running: [bwa mem -t 5 /data/broad/human_g1k_v37.fasta abra_temp_dir/all_contigs.fasta > abra_temp_dir/all_contigs.sam] [E::bwa_idx_load] fail to locate the index files Stream thread done. BWA time: 0 seconds. Exception in thread "main" java.lang.RuntimeException: BWA exited with non-zero return code : [1] for command: [bwa mem -t 5 /data/broad/human_g1k_v37.fasta abra_temp_dir/all_contigs.fasta > abra_temp_dir/all_contigs.sam] at abra.Aligner.runCommand(Aligner.java:66) at abra.Aligner.align(Aligner.java:36) at abra.ReAligner.alignAndCleanContigs(ReAligner.java:473) at abra.ReAligner.reAlign(ReAligner.java:181) at abra.ReAligner.run(ReAligner.java:1258) at abra.Abra.main(Abra.java:12) Stream thread done.

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The FASTA index file for "/data/broad/human_g1k_v37.fasta" exists, but not for "abra_temp_dir/all_contigs.fasta". I am using BWA version 0.7.9.

[mozack]

That message is from BWA and indicates that it cannot find the BWA index.

Have you run bwa index on /data/broad/human_g1k_v37.fasta ?

[Gig77]

yes, the index from the human reference is there, but the index for the abra generated FASTA file 'abra_temp_dir/all_contigs.fasta' is missing.

On Fri, Jun 13, 2014 at 1:34 PM, Lisle Mose notifications@github.com wrote:

That message is from BWA and indicatest that it cannot find the BWA index.

Have you run bwa index on /data/broad/human_g1k_v37.fasta ?

— Reply to this email directly or view it on GitHub https://github.com/mozack/abra/issues/5#issuecomment-46001248.

[mozack]

No index is necessary for all_contigs.fasta for that particular command. The all_contigs.fasta contigs are being aligned against the /data/broad/human_g1k_v37.fasta reference.

Can you post the output of the following here?

ls -lth /data/broad/human_g1k_v37.fasta*

[Gig77]

$:~/tools/abra-0.77$ ls -lth /data/broad/human_g1k_v37.fasta* -rwxr-xr-x 1 cf bioinformatics 2.7K Feb 5 16:06 /data/broad/human_g1k_v37.fasta.fai -rwxr-xr-x 1 cf bioinformatics 3.0G Feb 5 15:55 /data/broad/human_g1k_v37.fasta

But I see, I am missing the bwa indices! The index that is there was created with 'samtools faidx', not BWA. Will run 'bwa index' and see how it goes.

On Fri, Jun 13, 2014 at 3:49 PM, Lisle Mose notifications@github.com wrote:

No index is necessary for all_contigs.fasta for that particular command. The all_contigs.fasta contigs are being aligned against the /data/broad/human_g1k_v37.fasta reference.

Can you post the output of the following here?

ls -lth /data/broad/human_g1k_v37.fasta*

— Reply to this email directly or view it on GitHub https://github.com/mozack/abra/issues/5#issuecomment-46012945.

[mozack]

OK. Closing this - please do let me know if you run into any more issues.