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Gaius-Augustus / GUSHR

Generating UTRs from SHort Reads
GNU General Public License v3.0
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GUSHR error occurs at 752 and 660 #4

Closed tinyfallen closed 2 years ago

tinyfallen commented 2 years ago

Hi dear devolepers, I have ran the braker pipeline with --addUTR=on, and it failed at the GUSHR step

tail of the braker.log

# Tue Nov 9 20:49:41 2021: Adding UTRs to augustus.hints.gtf... # Tue Nov 9 20:49:41 2021: Running GUSHR... /export/home/ydn/.conda/envs/annotate/bin/python3 /export/home/ydn/yty/software/GUSHR/gushr.py -b /export/home/ydn/yty/aglaia/anno.before/braker_trans/ngs.bam -t /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/augustus.hints.gtf -g /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/genome.fa -o /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/gushr -c 48 -s /export/home/ydn/.conda/envs/yty/bin -a /export/home/ydn/.conda/envs/annotate/bin/ -j /export/home/ydn/.conda/envs/annotate/bin -q 2 > /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/gushr.log 2> /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/errors/gushr.err

the gushr.err

Traceback (most recent call last): File "/export/home/ydn/yty/software/GUSHR/gushr.py", line 752, in merge_original_with_utrs(args.gtf, utrs_gtf) File "/export/home/ydn/yty/software/GUSHR/gushr.py", line 660, in merge_original_with_utrs txid = re.search(r'transcript_id \"([^"]+)\"', line).group(1) AttributeError: 'NoneType' object has no attribute 'group'

If you need any other files to investigate the error, please tell me. Looking forward to your reply！

Best ~

KatharinaHoff commented 2 years ago

Thank you very much for reporting this issue. Regrettably it will take months until we can have a look at solving it.

Best,

Katharina

On Wed, Nov 10, 2021 at 4:28 AM tinyhys @.***> wrote:

Hi dear devolepers, I have ran the braker pipeline with --addUTR=on, and it failed at the GUSHR step

`# Tue Nov 9 20:49:41 2021: Adding UTRs to augustus.hints.gtf... Tue Nov 9 20:49:41 2021: Running GUSHR...

/export/home/ydn/.conda/envs/annotate/bin/python3 /export/home/ydn/yty/software/GUSHR/gushr.py -b /export/home/ydn/yty/aglaia/anno.before/braker_trans/ngs.bam -t /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/augustus.hints.gtf -g /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/genome.fa -o /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/gushr -c 48 -s /export/home/ydn/.conda/envs/yty/bin -a /export/home/ydn/.conda/envs/annotate/bin/ -j /export/home/ydn/.conda/envs/annotate/bin -q 2 > /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/gushr.log 2> /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/errors/gushr.err`

the gushr.err

Traceback (most recent call last): File "/export/home/ydn/yty/software/GUSHR/gushr.py", line 752, in merge_original_with_utrs(args.gtf, utrs_gtf) File "/export/home/ydn/yty/software/GUSHR/gushr.py", line 660, in merge_original_with_utrs txid = re.search(r'transcript_id \"([^"]+)\"', line).group(1) AttributeError: 'NoneType' object has no attribute 'group'

Looking forward to your reply！

Best ~

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tinyfallen commented 2 years ago

Thank you very much for reporting this issue. Regrettably it will take months until we can have a look at solving it. Best, Katharina … On Wed, Nov 10, 2021 at 4:28 AM tinyhys @.***> wrote: Hi dear devolepers, I have ran the braker pipeline with --addUTR=on, and it failed at the GUSHR step # Tue Nov 9 20:49:41 2021: Adding UTRs to augustus.hints.gtf... Tue Nov 9 20:49:41 2021: Running GUSHR... /export/home/ydn/.conda/envs/annotate/bin/python3 /export/home/ydn/yty/software/GUSHR/gushr.py -b /export/home/ydn/yty/aglaia/anno.before/braker_trans/ngs.bam -t /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/augustus.hints.gtf -g /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/genome.fa -o /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/gushr -c 48 -s /export/home/ydn/.conda/envs/yty/bin -a /export/home/ydn/.conda/envs/annotate/bin/ -j /export/home/ydn/.conda/envs/annotate/bin -q 2 > /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/gushr.log 2> /export/home/ydn/yty/aglaia/anno.before/braker_trans/braker/errors/gushr.err the gushr.err Traceback (most recent call last): File "/export/home/ydn/yty/software/GUSHR/gushr.py", line 752, in merge_original_with_utrs(args.gtf, utrs_gtf) File "/export/home/ydn/yty/software/GUSHR/gushr.py", line 660, in merge_original_with_utrs txid = re.search(r'transcript_id \"([^"]+)\"', line).group(1) AttributeError: 'NoneType' object has no attribute 'group' Looking forward to your reply！ Best ~ — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JGTI5X3QCTAKB5PYNDULHREXANCNFSM5HW3EYQQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Many thanks for your reply! I have found out what was wrong and it was all my fault. Once I edited the script gtf2gff.pl in the AUGUSTUS to make it output gff3 by default. I would never consider this minor modification would bring me sush a strange issue many days later!

Sorry for bothering!

Best ~