[E::hts_open_format] fail to open file about svaba

[walaj]

This looks like HTSlib is having trouble with the file. Can you try samtools index on it and see if it works? It also looks like there's a trailing backlash on the file name.

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On Jun 26, 2017, at 7:29 AM, rmurphy49 ***@***.***> wrote: Hello, I'm sure this is something small and insignificant but I am trying to run SvABA for the first time and the following command gives me the following error return: svaba/bin/svaba run -t /mnt/scratch/users/40057929/MCLHighNov2016/Batch1/04-0309-01-36351377/04-0309-01_S2.bam/ n- /mnt/scratch/users/40057929/MCL*/MCL*/12-2164*/12-2164-01_MRDneg_S1.bam/ -G /mnt/scratch/users/40057929/wg.fa/ -a svaba_Batch1_0309 -p 4 --- Running svaba SV and indel detection on 4 threads --- --- (inspect *.log for real-time progress updates) --- [E::hts_open_format] fail to open file '/mnt/scratch/users/40057929/MCLHighNov2016/Batch1/04-0309-01-36351377/04-0309-01_S2.bam/' ERROR: Cannot open main bam file: /mnt/scratch/users/40057929/MCLHighNov2016/Batch1/04-0309-01-36351377/04-0309-01_S2.bam/ I've checked the file path for the main tumour bam file and it is definitely correct. Any other advice? Let me know if you need any other information. Thanks, rmurphy49 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[rmurphy49]

Yeah the initial issue was a syntax error with the trailing backlash. Ran it again and it flags up the following error command:

svaba/bin/svaba run -t /mnt/scratch/users/40057929/MCLHighNov2016/Batch1/04-0309-01-36351377/04-0309-01_S2.bam n- /mnt/scratch/users/40057929/MCL*/MCL*/12-2164*/12-2164-01_MRDneg_S1.bam -G /users/40057929/wg.fa -a svaba_Batch1_0309 -p 4

--- Running svaba SV and indel detection on 4 threads ---
--- (inspect *.log for real-time progress updates) ---

[E::bwa_idx_load_from_disk] fail to locate the index files
ERROR: Unable to open index file: /users/40057929/wg.fa

Again, I've checked the file path and the index file is within the same directory. Thanks for the help so far I have little experience with Linux and any help would be great.

[walaj]

Your reference genome file "wg.fa" either doesn't exist or hasn't been indexed. You have to index the reference genome first with "bwa index" (the same as you would if you wanted to align reads to it with BWA). This creates some auxiliary files in the same directory that will be loaded by SvABA / BWA.

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On Wed, Jun 28, 2017 at 5:56 AM, rmurphy49 ***@***.***> wrote: Yeah the initial issue was a syntax error with the trailing backlash. Ran it again and it flags up the following error command: svaba/bin/svaba run -t /mnt/scratch/users/40057929/MCLHighNov2016/Batch1/04-0309-01-36351377/04-0309-01_S2.bam n- /mnt/scratch/users/40057929/MCL*/MCL*/12-2164*/12-2164-01_MRDneg_S1.bam -G /users/40057929/wg.fa -a svaba_Batch1_0309 -p 4 --- Running svaba SV and indel detection on 4 threads --- --- (inspect *.log for real-time progress updates) --- [E::bwa_idx_load_from_disk] fail to locate the index files ERROR: Unable to open index file: /users/40057929/wg.fa Again, I've checked the file path and the index file is within the same directory. Thanks for the help so far I have little experience with Linux and any help would be great. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#9 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGmfiMEJSsvdUsg4zZDTrPR8s8qEsmDjks5sIiM0gaJpZM4OFPj9> .

[rmurphy49]

This is my ls command output for the working directory the reference genome file is in:

hg19bwaidx.amb
hg19bwaidx.ann
hg19bwaidx.btw
hg19bwaidx.pac
hg19bwaidx.sa
wg.fa
wg.fa.fai

Would the different indexing filenames from wg.fa be the issue?

[walaj]

Yes that's the issue

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On Thu, Jun 29, 2017 at 5:47 AM, rmurphy49 ***@***.***> wrote: This is my ls command output for the working directory the reference genome file is in: hg19bwaidx.amb hg19bwaidx.ann hg19bwaidx.btw hg19bwaidx.pac hg19bwaidx.sa wg.fa wg.fa.fai Would the different indexing filenames from wg.fa be the issue? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#9 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGmfiN22kCc0bXjcIM2QbmRY4mdUr8qWks5sI3LIgaJpZM4OFPj9> .

[rmurphy49]

Changed the filenames to match the indexing filenames and still nothing. Any other advice that might help? I'm going to try and build the index again from scratch in case there are any errors. The reference genome I am using (standard hg19 genome) may be different from the genome used to reference the bam files I have been provided if this may give rise to any issue, although I believe the issue I have is related the finding the files.

[walaj]

Yes, I would rebuild the reference index with "bwa index" and use that file as the reference for SvABA. Using slightly difference reference genomes for SvABA vs original BAM shouldn't cause a problem.

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On Thu, Jun 29, 2017 at 8:48 AM, rmurphy49 ***@***.***> wrote: Changed the filenames to match the indexing filenames and still nothing. Any other advice that might help? I'm going to try and build the index again from scratch in case there are any errors. The reference genome I am using (standard hg19 genome) may be different from the genome used to reference the bam files I have been provided if this may give rise to any issue, although I believe the issue I have is related the finding the files. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#9 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGmfiEJK_BmI1awyZDwGo6LOTDn5yjpjks5sI50RgaJpZM4OFPj9> .

[rmurphy49]

The initial reference index was with bwa index, ran it again and still getting the same error message. All files with identical names and in the same directory. The command lines I used for bwa index were as follows:

bwa index -p hg19bwaidx -a bwtsw hg19bwaidx.fa
samtools faidx hg19bwaidx.fa

[walaj]

Is it still the "E::bwa_idx_load_from_disk" error? Could you try using the same index and aligning using BWA-MEM? The error it is showing is from the BWA part of the code, so that would be useful to know if that works.

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On Thu, Jul 6, 2017 at 8:18 AM, rmurphy49 ***@***.***> wrote: The initial reference index was with bwa index, ran it again and still getting the same error message. All files with identical names and in the same directory. The command lines I used for bwa index were as follows: bwa index -p hg19bwaidx -a bwtsw hg19bwaidx.fa samtools faidx hg19bwaidx.fa — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#9 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGmfiOkxr9aDnrpvjWULpjLY13TzOFLEks5sLNCpgaJpZM4OFPj9> .

[rmurphy49]

I obtained the reference fasta that was used for the alignment of the BAM file and this fixed the problem. This was also the case for other programs I am currently using which had similar issues to the one's I had described here. Thanks for the quick replies and help you have provided!