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Aligned Human Genome couldn't convert to Adam #1729

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Rokshan2016 opened this Issue Sep 16, 2017 · 5 comments

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@Rokshan2016

Rokshan2016 commented Sep 16, 2017

I did this steps-

  1. Index : Reference human genome using bow tie ( A. fna)
  2. Align : A. fna and A.fastq-- Done successfully--Got the output in A.fastq

When I am trying to convert A.fastq(Aligned) to adam , its not working .

Any suggestion will be helpful.

Thanks

@heuermh

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heuermh Sep 18, 2017

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When I am trying to convert A.fastq(Aligned) to adam , its not working .

What are you using for this step?

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heuermh commented Sep 18, 2017

When I am trying to convert A.fastq(Aligned) to adam , its not working .

What are you using for this step?

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Rokshan2016 Sep 18, 2017

  1. Index : I used Bow tie for index reference genome
  2. Alignment: data (.fastq ) with the indexed reference genome
    Output : .fastq file (Aligned with index)

But whenever I m trying to convert .fastq file (Aligned with index) to adam using the command:
./adam-submit transformAlignments hdfs://ip-10-48-3-5.ips.local:8020/user/rokshan.jahan/data/SRR1517848.fastq hdfs://ip-10-48-3-5.ips.local:8020/user/rokshan.jahan/SRR1517848.adam

It didnt give the correct parquet files inside .adam

Rokshan2016 commented Sep 18, 2017

  1. Index : I used Bow tie for index reference genome
  2. Alignment: data (.fastq ) with the indexed reference genome
    Output : .fastq file (Aligned with index)

But whenever I m trying to convert .fastq file (Aligned with index) to adam using the command:
./adam-submit transformAlignments hdfs://ip-10-48-3-5.ips.local:8020/user/rokshan.jahan/data/SRR1517848.fastq hdfs://ip-10-48-3-5.ips.local:8020/user/rokshan.jahan/SRR1517848.adam

It didnt give the correct parquet files inside .adam

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You shouldn't be getting a fastq file out of Bowtie, you should be getting a SAM file, so that part of the workflow looks suspicious. What error are you getting when you run transformAlignments?

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fnothaft commented Sep 18, 2017

You shouldn't be getting a fastq file out of Bowtie, you should be getting a SAM file, so that part of the workflow looks suspicious. What error are you getting when you run transformAlignments?

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Rokshan2016 Sep 18, 2017

I got the .adam . There was parquet files. But Data was not correct

Rokshan2016 commented Sep 18, 2017

I got the .adam . There was parquet files. But Data was not correct

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Rokshan2016 Sep 18, 2017

I used BWA for indexing and alignment
Did this steps:

  1. Indexed the reference genome
  2. Align the .fastq with the Indexed the reference genome and got the output as .sam
  3. Convert the .sam to .adam
    Output was correct
    But my concern is : I want to skip the .sam conversion,
    ** I want to align the .fastq with the Indexed reference genome and got the output as .adam

Is there any way I can do that?

Rokshan2016 commented Sep 18, 2017

I used BWA for indexing and alignment
Did this steps:

  1. Indexed the reference genome
  2. Align the .fastq with the Indexed the reference genome and got the output as .sam
  3. Convert the .sam to .adam
    Output was correct
    But my concern is : I want to skip the .sam conversion,
    ** I want to align the .fastq with the Indexed reference genome and got the output as .adam

Is there any way I can do that?

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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