kbsivakumar

ERROR ON UNZIPPING THE .gz file

3

python get_organelle_from_reads.py -1 Sample1.R1.fastq.gz -2 Sample1.R2.fastq.gz -o plastome_output -R 30 -k 21,45,65,85,105 -F embplant_pt --memory-save --reduce-reads-for-coverage inf --max-reads inf GetOrganelle v1.7.7.0 get_organelle_from_reads.py assembles organelle genomes from genome skimming data. Find...

error in classify.pl (no data in allele contig table)

2

blastn -query dip_cds.fa -db brapa.cds -out dr.blast.out -evalue 0.001 -outfmt 6 -num_threads 4 -num_alignments 5 perl [blastn_parse.pl](http://blastn_parse.pl/) -i dr.blast.out -o Edr.blast.out -q dip_cds.fa -b 1 -c 0.6 -d 0.8 perl...

python GenoDup.py File "/home/ubuntu/Documents/GenoDup-Pipeline/GenoDup.py", line 12 print 'You have to install related python modules' ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(...)?

MAKEFILE ERROR

1

$./configure Checking for 64 bits compiler... use CXX=g++ CFLAGS=-O3 -march=native binaries install to /home/ubuntu/bin tables install to /home/ubuntu/table alndbs install to /home/ubuntu/seqdb wrote Makefile wrote files OK. try make and...

Can't exec "/home/ubuntu/Documents/WGDdetector/bin/protein_mmseqs2_cluster.pl":

3

sh 00.run.sh Thursday 18 April 2024 04:26:57 PM IST ## phasing the raw input cds and pep Thursday 18 April 2024 04:26:58 PM IST ## running protein clustering ## Can't...

error installing singularity

3

Hi kindly help me to sort this out make -C builddir make: Entering directory '/home/ubuntu/go/src/github.com/sylabs/singularity-3.8.7/builddir' /bin/sh: 1: /home/ubuntu/go/src/github.com/sylabs/singularity-3.8.7/scripts/go-generate: Permission denied make: *** [Makefile:165: /home/ubuntu/go/src/github.com/sylabs/singularity-3.8.7/internal/pkg/buildcfg/config.go] Error 126 make: Leaving directory '/home/ubuntu/go/src/github.com/sylabs/singularity-3.8.7/builddir'

/home/ubuntu/anaconda3/lib/python3.11/site-packages/wgd-1.2-py3.11.egg/wgd/codeml.py:138: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy /home/ubuntu/anaconda3/lib/python3.11/site-packages/wgd-1.2-py3.11.egg/wgd/codeml.py:138: FutureWarning: Setting an item...

No reads in Hi-C contact matrices.

10

HELLO. my out.JBAT.log file generated is empty. (java -jar -Xmx32G juicer_tools.1.9.9_jcuda.0.8.jar pre out_JBAT.txt out_JBAT.hic.part

Undefined subroutine &main::prepare_gffout called at agat_convert_sp_gxf2gxf.pl line 52.

1

hi I have installed agat manually from github. Im trying to do gtf to gff3 conversion. perl agat_convert_sp_gxf2gxf.pl -g braker.gtf -o br ------------------------------------------------------------------------------ | Another GFF Analysis Toolkit (AGAT) -...

compilation issue

11

Building CXX object src/CMakeFiles/raxml_module.dir/CommandLineParser.cpp.o make[2]: *** [src/CMakeFiles/raxml_module.dir/build.make:76: src/CMakeFiles/raxml_module.dir/AncestralStates.cpp.o] Error 127 /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found make[2]: *** [test/src/CMakeFiles/raxml_test_module.dir/build.make:90: test/src/CMakeFiles/raxml_test_module.dir/__/__/src/Checkpoint.cpp.o] Error 127