Jeffrey Godwin

There is some error in decompression of trimmomatic putput files through gzip. Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /media/hd1/BS_seq_test1/2_results1/trimmomatic-files/Sample1_paired_1.fastq.gz and /media/hd1/BS_seq_test1/2_results1/trimmomatic-files/Sample1_paired_2.fastq.gz **gzip: stdout:...

Hi Rashmi, Thanks for getting back. I will try with fewer CPU threads. Is there an issue with using samtools 1.12. The installation guide mentions samtools (Ver. > 1.9 )....

I'm having the same issue. Following this thread for a solution. Thanks in advance, Jeff

Hi @fransua, Thank you for the reply. I ran tadbit map with --renz MboI Hinfl and --renz MboI DpnII HinfI and it produced the following error - Writing log to...

It appears the "HinfI" enzyme (STRING) is the issue. Any other combinations of enzymes proceeds normally. Running with just --renz HinfI produces the same error as above Curiously it does...

My TADbit version is v1.1 I'm attaching my bash script for your reference - fastq_dir="/home/jgodwin/Data/Hi-C/RK_data/1_Raw_data" workdir="/home/jgodwin/Data/Hi-C/RK_data/2_Tadbit_Out" yeast_ref="/home/jgodwin/Data/Hi-C/Yeast_ref" tadbit map -w ${workdir} --fastq ${fastq_dir}/WT_L1_1.dsrc --read 1 --index ${yeast_ref}/sacCer3.gem --renz DpnII HinfI...

Unfortunately the problem exists after re-installation too. **Running with MboI and HindIII proceeds without a problem. Attaching the log here -** Writing log to /home/jgodwin/Data/Hi-C/RK_data/2_Tadbit_Out/process.log Writing versions of TADbit and...

It appears it's a problem with the reads. The mapping proceeds with the demo data used for the 3DARORC tutorial (SRR5077821) without a problem. I'm rechecking the reads although I...

Hi Francois, The same issue shows up with the new index as well. My read lengths are the same (35bp - wonder if this is tripping something). I tried mapping...

@TheTams This solution works for a conda environment (R 4.1.3). Thanks