PAScall error

[Yunlu-Zhu]

I ran the following command:

```bash
scapture -m PAScall -a SCAPTURE_annotation -g genome.fa -b PBMC3k.test.bam -l 98 -o PBMC3k -p 16 --species human --polyaDB SupTab_KnownPASs_fourDBs.txt &> PBMC3k.PAScall.log

But received the following errors:

1. Parallel command not found:

   /data1/A01/2023222612/yunlu_zhu/apa_s92/SCAPTURE-main/scapture:行217: parallel: 未找到命令
   

2. Missing temporary files:

   sort: 无法读取: PBMC3k_tmp/PBMC3k.exonic.peak.isoform.tmp: 没有那个文件或目录
   rm: 无法删除'PBMC3k_tmp/PBMC3k.exonic.peak.isoform.tmp': 没有那个文件或目录
   

3. Inconsistent naming convention warnings:

   ***** WARNING: File SCAPTURE_annotation.genetype.bed has inconsistent naming convention for record:
   GL000008.2 83331 200303 ENSG00000296732|lncRNA|ENST00000741402.1 0 + 200303 200303 0 3 214,59,876, 0,2235,116096,
   

4. Missing commands (bedToGenePred, genePredToBed):

   /data1/A01/2023222612/yunlu_zhu/apa_s92/SCAPTURE-main/scapture:行264: bedToGenePred: 未找到命令
   /data1/A01/2023222612/yunlu_zhu/apa_s92/SCAPTURE-main/scapture:行264: genePredToBed: 未找到命令
   

5. Missing Predict_Result.txt files:

   cat: PBMC3k.exonic.peaks.DeepPASS.predictout/Predict_Result.txt: 没有那个文件或目录
   Error: unable to open file or unable to determine types for file -
   

6. Output files generated:

   scapture PAScall: output files --  PBMC3k.exonic.peaks.evaluated.bed PBMC3k.intronic.peaks.evaluated.bed PBMC3k.3primeExtended.peaks.evaluated.bed
   

Any help or suggestions would be greatly appreciated!

```