icbi-lab / merantk Goto Github PK

Dear Prof. Dietmar Rieder,

I downloaded the latest version of meRanTK(1,3,0) and installed with "the easy way". While running meRanGs align on the server of our lab (CentOS 8), I kept encountering this ERROR: “Can't locate object method "new" via package "GD::Graph::lines" at script/meRanGh.pl line 4807.

However, I already installed GD and GDGraph. To make sure of this, I wrote a simple perl scrip called test.pl (use GD::Graph::lines), and run perl test.pl, there is no warning and errors. In the directory of perl , I could find GD/Graph/lines.pm, and GD/GD.pm, etc.

I've been stuck on this for quit a few days, I've tried to re-install perl and GD and other required modules for m bias plot. But none of these get work.

I would be really appreciated if meRanTK developer team members could provide some other methods to solve this. Thanks for your effort on this great toolkit.

Best Regards

At the first execution meRanCall worked properly, but when executing again it returns an "Illegal instruction (core dump)" error.
The same thing occurred to other members from my lab.
We found out that at the first execution meRanCall generates a file "/tmp/par-*" that, once removed, allows for a new execution of the tool.
This behaviour repeats itself after every execution.

Thanks for your toolkits, I encountered some error.
My code

meRanGs mkbsidx -t 32 -fa Mus_musculus.GRCm38_and_ctrl.fa -id ctrl_bsgenomeidx -GTF Mus_musculus.GRCm38.87_standard.gtf

meRanGs align -o ../../map_results/CK_WT1 -f CK_WT1.clean.R1.fastq.gz -r CK_WT1.clean.R2.fastq.gz -t 6 -S RNA-BSseq.sam -id /project/yinjiakang/KC2022-G0761/refseq/ctrl_bsgenomeidx -mbp -star_outFilterMultimapNmax 20 -MM -d

The fatal error is

can't mkfifo ../../map_results/CK_WT1/meRanGs_FQ_spooler_fwd_50967: Function not implemented at script/meRanGs.pl line 1265.

Would you be kind to help? Thanks in advance.
meRanGs_C2T_50967_star_Log.out.txt

When using meRanGs mkbsidx, the SAindex (k-mer index) generation is taking much more time for C->T or G ->A genome, which, in hindsight, should have been obvious. SAindex contains the positions of all k=14-mers in the suffix array. With one base missing, a lot of k-mers will be mssing, which slows down the calculation significantly.
Please see the STAR issue: alexdobin/STAR#1263

Dear Prof. Dietmar Rieder,

Thanks for your toolkits. I have been trying to use meRanTK to process my RNA data. I used meRanGh to map and and meRanCall to call m5C sites. I noticed that the default value of '-minC|-mc' is 3, could you please tell me why is 3? and can it be 1 or 0? I attempted to set the value to 0 to test its limits; however, I encountered the following error:

Use of uninitialized value in subtraction (-) at /path/to/softwares/meRanTK/src/meRanCall.pl line 1483.

when I adjusted the '-minC|-mc' value to 1, these errors did not occur.

And I have discovered zero values in total C counts in my bisulfite data
chrom start strand pos methy unmethy count ratio
chr10 10734 - 10734 4 0 4 1.0 1.0 0.0 0.0 3
chr10 10738 + 10738 4 0 4 1.0 1.0 0.0 0.0 3
chr10 10739 - 10739 6 0 6 1.0 1.0 0.0 0.0 3
chr10 10741 + 10741 5 0 5 1.0 1.0 0.0 0.0 3
chr10 10742 - 10742 7 0 7 1.0 1.0 0.0 0.0 3
chr10 10744 + 10744 6 0 6 1.0 1.0 0.0 0.0 3

Thank you very much for your time and assistance. I look forward to your response.

Best Regards

Hello, I have been trying to use MeRanTK to align my paired end BS-RNA-Seq reads but I am getting extremely low alignment % (somewhere around ~0.05%). Here is my call:

~/software/meRanTK/meRanGh.pl align \                                                                                                                                              ─╯
            -o test/meRanGhResult \
            -f RB_WT1_S1_L001_R1_001.fastq \
            -r RB_WT1_S1_L001_R2_001.fastq \
            -t 10 \
            -S test_RNA_BSseq.sam \
            -GTF gencode.v44.annotation.gtf \
            -id transcriptome_Gh_hisat_built \
            -dt \

When I use hisat3n to align my reads, I get much better alignment ~60%. If I try to use the bam retrieved from hisat3n on meRanCall, I seem to be stuck at the processing stage:

processing 706 sequences: [KI270757.1 - 100.00%] [overall - 100.00%] done ...