erro on test

Question

erro on test

Closed this issue 2 years ago · 6 comments

I try to run the insertion test and I get this erro

"""
/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/TEMP2_insertion.sh: 第 206 行:[: -: 期待整数表达式
sort: cannot read: test.supportReads/*.bed: 没有那个文件或目录

***** ERROR: Requested column 4, but database file - only has fields 1 - 0.
Traceback (most recent call last):
File "/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/processMergedBed.py", line 108, in
main()
File "/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/processMergedBed.py", line 10, in main
tel = int(sys.argv[2])
IndexError: list index out of range
merge support reads in different direction within 2 X - 2022年 06月 13日星期一 09:45:06 CST
cat: test.supportReads/*.final.bed: 没有那个文件或目录
"""

this is my command
"TEMP2 insertion -l test.1.fastq.gz -r test.2.fastq.gz -I bwa_index/chr2L -g chr2L.fa -R transposon.fa -t rmsk.bed -o test_output -c 2"

the test.insertion.bed only have the head line but without any data .

Answer 1 · 2022-06-14T01:50:51.000Z

Attachment:
[caoshuo@login1 tmpTEMP2]$ ls test.supportReads/
*.merged.bed *.processed.bed

thanks!!!

Answer 2 · 2022-06-14T12:59:05.000Z

Can you upload the entire log file? Thanks!

Answer 3 · 2022-06-14T13:14:52.000Z

here is my log file

err.log
out.log

thanks!
shuo cao

Answer 4 · 2022-06-14T13:37:08.000Z

It looks like you don't have R installed in your machine.

Answer 5 · 2022-06-15T01:29:35.000Z

thanks! I thought R was just for drawing.

I have successfully installed R-base, but there still have some errors

"""

***** ERROR: Requested column 4, but database file - only has fields 1 - 0.

***** ERROR: Requested column 4, but database file - only has fields 1 - 0.
/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/TEMP2_insertion.sh:行207: ${i/.bed/.merged.bed}: 模糊的重定向

***** ERROR: Requested column 4, but database file - only has fields 1 - 0.

***** ERROR: Requested column 4, but database file - only has fields 1 - 0.
/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/TEMP2_insertion.sh:行210: ${i/merged.bed/processed.bed}: 模糊的重定向
Traceback (most recent call last):
File "/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/processMergedBed.py", line 108, in
main()
File "/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/processMergedBed.py", line 10, in main
tel = int(sys.argv[2])
ValueError: invalid literal for int() with base 10: 'test.supportReads/*.merged.merged.merged.bed'
Traceback (most recent call last):
File "/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/processMergedBed.py", line 108, in
main()
File "/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/processMergedBed.py", line 11, in main
ins = int(sys.argv[3])
IndexError: list index out of range
Traceback (most recent call last):
File "/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/processMergedBed.py", line 108, in
main()
File "/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/processMergedBed.py", line 11, in main
ins = int(sys.argv[3])
IndexError: list index out of range
/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/TEMP2_insertion.sh:行210: ${i/merged.bed/processed.bed}: 模糊的重定向
Traceback (most recent call last):
File "/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/processMergedBed.py", line 108, in
main()
File "/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/processMergedBed.py", line 11, in main
ins = int(sys.argv[3])
IndexError: list index out of range
Traceback (most recent call last):
File "/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/processMergedBed.py", line 108, in
main()
File "/public/agis/zhouyongfeng_group/caoshuo/tools/TEMP2/bin/processMergedBed.py", line 11, in main
ins = int(sys.argv[3])
IndexError: list index out of range
"""
and there is the output file

thanks for your reply!!! wish you have a good day~

cao

Answer 6 · 2022-11-08T20:24:05.000Z

Hi cao, sorry for the late reply. I hope you have solved the issue. If not, it is probably due to the version of samtools, you might want to try install samtools with version ≥ 1.9 to see if it works. I will close thread.