WrightonLabCSU
error with DRAM-v distill
Hi,
I have already finished the annotation step and get the annotations.tsv file, now I am doing the distill. step. Here is my command line "DRAM-v.py distill -i annotations.tsv -o distilled2". However, I got the error. Please see the below message.
"Traceback (most recent call last):
File "/software/anaconda3/envs/DRAM/bin/DRAM-v.py", line 140, in
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/software/anaconda3/envs/DRAM/bin/DRAM-v.py", line 140, in
Could you help me to figure out what is going on?
Best,
Qi
Here is the column name of "annotation.tsv" file : "fasta" "scaffold"
[3] "gene_position" "start_position"
[5] "end_position" "strandedness"
[7] "rank" "kegg_id"
[9] "kegg_hit" "viral_id"
[11] "viral_hit" "viral_RBH"
[13] "viral_identity" "viral_bitScore"
[15] "viral_eVal" "peptidase_id"
[17] "peptidase_family" "peptidase_hit"
[19] "peptidase_RBH" "peptidase_identity"
[21] "peptidase_bitScore" "peptidase_eVal"
[23] "pfam_hits" "cazy_hits"
[25] "vogdb_description" "vogdb_categories"
[27] "heme_regulatory_motif_count"
Hi Qiqi04Tsinghua, I got the same KeyError: 'amg_flags' error when I ran a DRAM-v.py distill command on an annotations.tsv that was produced using DRAM.py annotate. If you're trying to distill a DRAMv run make sure you use DRAM-v.py distill. If you're trying to distill a regular DRAM run, make sure you use DRAM.py distill. In other words, you can't distill annotations from a regular DRAM run using DRAMv b/c DRAM-v.py distill expects the amg_flags column to be present in the annotations. I hope that helps
Hi WrightonLabCSU,
Thank you for reminding and explanation!
Best,
Qi
------------------ 原始邮件 ------------------ 发件人: "WrightonLabCSU/DRAM" @.>; 发送时间: 2024年3月5日(星期二) 凌晨1:02 @.>; @.@.>; 主题: Re: [WrightonLabCSU/DRAM] error with DRAM-v distill (Issue #270)
Hi Qiqi04Tsinghua, I got the same KeyError: 'amg_flags' error when I ran a DRAM-v.py distill command on an annotations.tsv that was produced using DRAM.py annotate. If you're trying to distill a DRAMv run make sure you use DRAM-v.py distill. If you're trying to distill a regular DRAM run, make sure you use DRAM.py distill. In other words, you can't distill annotations from a regular DRAM run using DRAMv b/c DRAM-v.py distill expects the amg_flags column to be present in the annotations. I hope that helps
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