Philge Philip

error, no valid sequences were found

1

I get below output in file "GeneMark-ET.stdout" when I run following BRAKER command "braker.pl \ --gff3 \ --overwrite \ --species=Bat \ --cores=48 \ --genome=scaffolds_FINAL.fasta \ --bam=./direct_inference_out/merged.bam,/data_all/annotation/scaffolds/iso-seq/hq_isoforms.fasta.sorted.bam" [braker.log](https://github.com/Gaius-Augustus/BRAKER/files/7559186/braker.log) check before the...

invalid literal for int() with base 10: '1307=1' and UserWarning: Problem parsing transcript with ID 'transcript/10670'

3

Hi, I am getting issues like below when I run TranscriptClean "Correcting transcripts... invalid literal for int() with base 10: '1307=1' invalid literal for int() with base 10: '15=1' invalid...

Error while expanding /RDPTools/classifier/build/classes/data.tgz

2

Error while expanding /RDPTools/classifier/build/classes/data.tgz java.io.EOFException: Unexpected end of ZLIB input stream at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240) at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158) at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:117) at org.apache.tools.tar.TarBuffer.readBlock(TarBuffer.java:253) at org.apache.tools.tar.TarBuffer.readRecord(TarBuffer.java:220) at org.apache.tools.tar.TarInputStream.read(TarInputStream.java:603) at java.io.FilterInputStream.read(FilterInputStream.java:107) at org.apache.tools.ant.taskdefs.Expand.extractFile(Expand.java:358) at org.apache.tools.ant.taskdefs.Untar.expandStream(Untar.java:163) at...

Hi, if we provide Genome alignment between the reference and query genome(s), wont Toga annotate each query genome and give the output? In that case will it be faster than...