No output in final_results

[KunFang93]

Hi,

I met a problem that there is no output results for some of my samples. The error message shows:

Making Immunogenicity prediction
(None, 256)
Making Neoantigen Filtering
usage: seq2neo [-h] {whole,immuno,download} ...

A pipeline from mutation to neoantigen prediction

positional arguments:
  {whole,immuno,download}
    whole               Run whole pipeline(Seq2Neo) with fastq/bam/sam file
    immuno              Run immunogenicity prediction with peptides
    download            downloading reference genome

optional arguments:
  -h, --help            show this help message and exit

Thanks for using Seq2Neo
Error: No command specified

There are some results in results folder:

(Seq2Neo) [root@9ac92c70ddc8 results]# ls
Aligned.out.sorted_genes.ent                 Patient400_T5_Tumor_mrna_pre.fasta          Patient400_T5_Tumor_tmpgenefusion_9.fasta  dictionary_wt_mt.txt
Aligned.out.sorted_genes.out                 Patient400_T5_Tumor_pre.fasta               Patient400_T5_Tumor_tmpindel_10.fasta      fusion.fasta
Aligned.out.sorted_genes.uni                 Patient400_T5_Tumor_tmp_10.fasta            Patient400_T5_Tumor_tmpindel_11.fasta      fusion_tmp.fasta
Patient400_T5_Tumor.exonic_variant_function  Patient400_T5_Tumor_tmp_11.fasta            Patient400_T5_Tumor_tmpindel_8.fasta       neo
Patient400_T5_Tumor.fasta                    Patient400_T5_Tumor_tmp_8.fasta             Patient400_T5_Tumor_tmpindel_9.fasta       pass.recode.vcf
Patient400_T5_Tumor.log                      Patient400_T5_Tumor_tmp_9.fasta             agfusion_dir                               variant.Patient400_Normal.avinput
Patient400_T5_Tumor.variant_function         Patient400_T5_Tumor_tmpgenefusion_10.fasta  dictionary.txt                             variant.Patient400_T5_Tumor.avinput
Patient400_T5_Tumor_final.result.txt         Patient400_T5_Tumor_tmpgenefusion_11.fasta  dictionary_fusion.txt
Patient400_T5_Tumor_mrna.fasta               Patient400_T5_Tumor_tmpgenefusion_8.fasta   dictionary_mrna.txt

I wondered how could I solve this problem? Thanks for your help!

Best, Kun

[diaokx]

Sorry for that, there may be a problem in the intermediate process.