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Error running eagle #3

Closed signor-molevol closed 4 years ago

signor-molevol commented 4 years ago

ERROR: (eagle.c:176: errno: None) failed to find 3 in reference

If you have any idea what the issue might be. Error is rather opaque. Reference has the chromosomes it is supposed to, is the right reference.

./eagle --splice -v variants.vcf -a reads.bam -r reference.fasta > eagletest

tony-kuo commented 4 years ago

The error is stating it failed to find "3" in the reference index. I'm assuming there is a chromosome named >3 in the reference. Can you show contents of the fasta index file (i.e. reference.fasta.fai)?

signor-molevol commented 4 years ago

It is called 3L and 3R. Are letters in chromosome names not supported?

From: Tony Kuo notifications@github.com Sent: Wednesday, February 19, 2020 8:16 PM To: tony-kuo/eagle eagle@noreply.github.com Cc: Sarah Signor ssignor@usc.edu; Author author@noreply.github.com Subject: Re: [tony-kuo/eagle] Error running eagle (#3)

The error is stating it failed to find "3" in the reference index. I'm assuming there is a chromosome named >3 in the reference. Can you show contents of the fasta index file (i.e. reference.fasta.fai)?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tony-2Dkuo_eagle_issues_3-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DAFIPZVZH6RX47Z7K5EB7I73RDWHTDA5CNFSM4KYAMNIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMJLEZA-23issuecomment-2D588427876&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ai4jwsjE16fpmwgsSJVp9g&m=tHopzwj47bpeGWHinj9Fy_DM6kRO-usHlpSLjYV5Qtc&s=-HevA_2tFF_h70yLUFcZaI1KF23eUYQDqaRCCqGHJ8Q&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AFIPZV2IEZWDYNWSASF7W2TRDWHTDANCNFSM4KYAMNIA&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ai4jwsjE16fpmwgsSJVp9g&m=tHopzwj47bpeGWHinj9Fy_DM6kRO-usHlpSLjYV5Qtc&s=n8jx73N6gSS99ECpE259QggroOgHGRGb5mTem-wkjd4&e=.

signor-molevol commented 4 years ago

From: Sarah Signor ssignor@usc.edu Sent: Wednesday, February 19, 2020 9:00 PM To: tony-kuo/eagle reply@reply.github.com Subject: Re: [tony-kuo/eagle] Error running eagle (#3)

It is called 3L and 3R. Are letters in chromosome names not supported?

From: Tony Kuo notifications@github.com Sent: Wednesday, February 19, 2020 8:16 PM To: tony-kuo/eagle eagle@noreply.github.com Cc: Sarah Signor ssignor@usc.edu; Author author@noreply.github.com Subject: Re: [tony-kuo/eagle] Error running eagle (#3)

The error is stating it failed to find "3" in the reference index. I'm assuming there is a chromosome named >3 in the reference. Can you show contents of the fasta index file (i.e. reference.fasta.fai)?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tony-2Dkuo_eagle_issues_3-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DAFIPZVZH6RX47Z7K5EB7I73RDWHTDA5CNFSM4KYAMNIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMJLEZA-23issuecomment-2D588427876&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ai4jwsjE16fpmwgsSJVp9g&m=tHopzwj47bpeGWHinj9Fy_DM6kRO-usHlpSLjYV5Qtc&s=-HevA_2tFF_h70yLUFcZaI1KF23eUYQDqaRCCqGHJ8Q&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AFIPZV2IEZWDYNWSASF7W2TRDWHTDANCNFSM4KYAMNIA&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ai4jwsjE16fpmwgsSJVp9g&m=tHopzwj47bpeGWHinj9Fy_DM6kRO-usHlpSLjYV5Qtc&s=n8jx73N6gSS99ECpE259QggroOgHGRGb5mTem-wkjd4&e=.

tony-kuo commented 4 years ago

Letters in chromosomes are supported. There is something directly referring to chromosome 3. Can you check your VCF file to see if there are chromosomes that are not in the reference?

cut -f1 variants.vcf | sort | uniq will give you a quick peak at chromosomes in your vcf

signor-molevol commented 4 years ago

You are absolutely right, the names of the chromosomes were screwed up during the process by the GATK alternate reference maker. Sorry to take your time!

tony-kuo commented 4 years ago

No problem. Glad we could figure out the issue.