ValueError: Expected object or value

[yuxinPenny]

I came up with following error while running the spore diffmod. The nanopolish eventalign and data-prep output seems no problem. Can you give some clues?

Traceback (most recent call last): File "/home/yuxin/miniconda3/bin/xpore", line 8, in sys.exit(main()) File "/home/yuxin/miniconda3/lib/python3.8/site-packages/xpore/scripts/xpore.py", line 67, in main options.func(options) File "/home/yuxin/miniconda3/lib/python3.8/site-packages/xpore/scripts/diffmod.py", line 169, in diffmod data_dict[(condition_name,run_name)] = ujson.loads(json_str) # A data dict for each gene. ValueError: Expected object or value

PS. code to for nanopolish event align and data prep

/home/yuxin/minimap2-2.17_x64-linux/minimap2 -ax map-ont \ /data/yuxin/2021Fall/Reference/HomoSapiens/gencode.v29.transcripts_simplified.fa \ /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/fastq/HMEC_WT_fastq.tar.gz > \ /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/bam/HMEC_WT_t.sam -t 6

samtools view -b \ -S /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/bam/HMEC_WT_t.sam > \ /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/bam/HMEC_WT_t.bam

sort

samtools sort \ /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/bam/HMEC_WT_t.bam \ -o /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/bam/HMEC_WT_t.bam

index

samtools index \ /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/bam/HMEC_WT_t.bam \ /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/bam/HMEC_WT_t.bam.bai

cd /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/fastq/workspace/pass find -maxdepth 5 -name "*.fastq"|xargs -i awk \ '{if(NR%4 == 1){print ">" substr($0, 2)}}{if(NR%4 == 2){print}}' {} |cat > \ /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/xpore_result/HMEC_WT_reads.fasta

index

/home/yuxin/nanopolish/nanopolish index -d /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/fast5_single_pass \ /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/xpore_result/HMEC_WT_reads.fasta

event align

/home/yuxin/nanopolish/nanopolish eventalign \ --reads /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/xpore_result/HMEC_WT_reads.fasta \ --bam /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/bam/HMEC_WT_t.bam \ --genome /data/yuxin/2021Fall/Reference/HomoSapiens/gencode.v29.transcripts_simplified.fa \ --scale-events > /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/xpore_result/reads-ref.eventalign.txt \ -t 5

xpore dataprep \ --eventalign /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/xpore_result/reads-ref.eventalign.txt \ --out_dir /data/yuxin/2021Fall/HomoSapiens/HMEC/HMEC_WT/xpore_result \ --n_processes 6

[yuxinPenny]

By the way, I didn't run the nanopolish eventalign step with nohup or &

[yuukiiwa]

Hi @yuxinPenny,

I am so sorry for the delayed reply (I thought someone else answered the question as I see there's a comment already). Do you mind sharing the config.yml file you used for running xpore diffmod, please?

There are several possibilities that can cause ValueError: Expected object or value. Here are several things you can check:

• [ ] Whether the paths to the dataprep directories exist
• [ ] Whether you have enough storage space to output the dataprep/data.json file as ujson does not work if a json file is malformed

Thanks!

Best wishes, Yuk Kei