Comments (7)
ANGSD
commented on August 16, 2024
Pushed a new version that should fix this issue.
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martinsikora
commented on August 16, 2024
Hi,
it seems it's still not fixed, now I get same error with other reads. E.g.
metadamage getdamage -p 25 -r1 bam/BH75-55/31242.globodera_pallida.PRJEB123.WBPS15.botgarden.hum_eupathDB.filter.bam -o metadamage/BH75-55/31242.globodera_pallida.PRJEB123.WBPS15.botgarden.hum_eupathDB.filter #metadamage getdamage -p 25 -r1 bam/BH75-55/31242.globodera_pallida.PRJEB123.WBPS15.botgarden.hum_eupathDB.filter.bam -o metadamage/BH75-55/31242.globodera_pallida.PRJEB123.WBPS15.botgarden.hum_eupathDB.filter
./metadamage refName: (null) minLength: 35 printLength: 25 runmode: 1 outname: metadamage/BH75-55/31242.globodera_pallida.PRJEB123.WBPS15.botgarden.hum_eupathDB.filter nthreads: 4 Could not recreate the sequence for read: M_A00706:67:HGMMWDSXX:4:2110:31864:19820
samtools view bam/BH75-55/31242.globodera_pallida.PRJEB123.WBPS15.botgarden.hum_eupathDB.filter.bam | grep "M_A00706:67:HGMMWDSXX:4:2110:31864:19820"
M_A00706:67:HGMMWDSXX:4:2110:31864:19820 16 pathogens_Gpal_scaffold_18 346300 23 23S69M * 0 0 CCTCGATCGTCGGCCGCCCGCGCCACCAGGGCGTCATGGTCGGCATGGGCCAGAAGGACGCGTACGTGGGCGATGAAGCCCAGTCCAAGCGG JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ s1:i:41 s2:i:33 PG:Z:MarkDuplicates RG:Z:31242.BH75-55 NM:i:4 AS:i:106 de:f:0.058 rl:i:0 cm:i:5 nn:i:0 tp:A:P ms:i:106 MD:Z:47G2C2G14T0
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martinsikora
commented on August 16, 2024
update, it failed on other files too, so I went back to commit 787087b which fixed the new issue. So it seems the original fix broke it in another way
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ANGSD
commented on August 16, 2024
Could I obtain a copy of the offending file?
… On 8 Feb 2021, at 10.55, martinsikora ***@***.***> wrote:
update, it failed on other files too, so I went back to commit 787087b <787087b> which fixed the new issue. So it seems the original fix broke it in another way
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martinsikora
commented on August 16, 2024
that work?
34507.steinernema_feltiae.PRJNA353610.WBPS15.botgarden.hum_eupathDB.filter.bam.gz
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ANGSD
commented on August 16, 2024
Ok please try the most recent, there was a bug that was introduced in one of the more recent versions. It should work now.
Best
… On 8 Feb 2021, at 12.10, martinsikora ***@***.***> wrote:
that work?
34507.steinernema_feltiae.PRJNA353610.WBPS15.botgarden.hum_eupathDB.filter.bam.gz <https://github.com/ANGSD/metadamage/files/5943234/34507.steinernema_feltiae.PRJNA353610.WBPS15.botgarden.hum_eupathDB.filter.bam.gz>
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martinsikora
commented on August 16, 2024
looks to work now, thanks!
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Related Issues (20)
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