KeyError: "tag 'MD' not present"

[mochew]

Hi there,

I encountered a KeyError exception when running NanoSim. Specifically, the error report KeyError: "tag 'cs' not present". This error occurred during the execution of the script when trying to analyze reads and match error models. Below is the full traceback from the log.

Could you please help me resolve this issue? Thank you for your assistance!

[lcoombe]

Hi @mochew,

Could you provide us with a bit more information, including:

• Version of NanoSim installed
• How you installed NanoSim and dependencies (ex. conda, source code, etc)
• Version of minimap2 installed
• Your full command

Thank you for your interest in NanoSim!
Lauren

[mochew]

Thank you for your response. The commands I used to install NanoSim are as follows:

（1）git clone https://github.com/bcgsc/NanoSim.git
（2）conda create --name nanosim python=3.7
（3）conda activate nanosim
（4）conda install --file requirements.txt -c conda-forge -c bioconda
（5）conda install regex
The commands I used to run NanoSim are as follows:

nohup python read_analysis.py genome
-i /newhome/Public_data/TRs/DeepTR-source-data/HG001/Nanopore/HG001_Circulomics_Guppy_4.2.2.fastq.gz
-ga /home/wuyingfu/complete_sequence/ref_sequence/GCA_009914755.4_T2T-CHM13v2.0_genomic.fna_exten_TR_intrv_align/HG001/HG001_Nanopore_aln_sorted.bam
-o /home/wuyingfu/complete_sequence/Nanosim/Out_put/
-t 40

/home/wuyingfu/complete_sequence/Nanosim/log/analysis_HG001_reads.log 2>&1 &

The library versions in the NanoSim environment are shown in the figure below：

If you need any further information, please let me know. I look forward to your response

[mochew]

In addition, the minimap2 I installed is as follows:

[lcoombe]

Hi @mochew,

A couple suggestions:

• We highly recommend installing NanoSim fully from conda, ideally in a fresh conda environment: conda install -c conda-forge -c bioconda nanosim -> this is just easier and leads to more consistent/reliable installations
• You have supplied your own BAM file to NanoSim. You need to ensure that in that alignment file, CS tags are present (by specifying --cs option to your minimap2 alignment command). More information can be found here: https://github.com/bcgsc/NanoSim?tab=readme-ov-file#usage. A good option is to let NanoSim do the alignment for you, instead of supplying the BAM file, so that you don't have to consider the alignment arguments.

[mochew]

Thank you very much for your response. I will try running NanoSim again based on your suggestions.