weng-lab/TEMP2

Error on test data

Closed this issue · 1 comments

Partlycloudy029 commented

Hi,
When I run the program on test data, unfortunately I have some problems,it shows that message:

Testing required softwares:
bwa: /public/software/env01/bin/bwa
samtools: /public/software/env01/bin/samtools
bedtools: /public/software/env01/bin/bedtools
------ Start pipeline ------
bam file not specified, map raw reads tp genome via bwa mem Sat Jul 8 15:07:01 CST 2023
transform sam to sorted bam and index it Sat Jul 8 15:07:15 CST 2023
get concordant-uniq-split reads Sat Jul 8 15:07:19 CST 2023
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 0 reads
check fragment length Sat Jul 8 15:07:22 CST 2023
/public/home/soft/TEMP2-master/bin/TEMP2_insertion.sh: line 169: Rscript: command not found
insert size set to 95 quantile:
/public/home/soft/TEMP2-master/bin/TEMP2_insertion.sh: line 172: [: -gt: unary operator expected
get mate seq of the uniq-unpaired Sat Jul 8 15:07:23 CST 2023
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 0 reads
map paired split uniqMappers and unpaired uniqMappers to transposons Sat Jul 8 15:07:23 CST 2023
merge fragments in genome and transposon Sat Jul 8 15:07:24 CST 2023
test.t is empty
merge support reads in the same direction within - Sat Jul 8 15:07:26 CST 2023
/public/home/zhangtianhao/soft/TEMP2-master/bin/TEMP2_insertion.sh: line 208: [: -: integer expression expected
sort: cannot read: test.supportReads/*.bed: No such file or directory

***** ERROR: Requested column 4, but database file - only has fields 1 - 0.
Traceback (most recent call last):
File "/public/home/soft/TEMP2-master/bin/processMergedBed.py", line 108, in
main()
File "/public/home/soft/TEMP2-master/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 - Sat Jul 8 15:07:27 CST 2023
filter candidate insertions which overlap with the same transposon insertion or in high depth region Sat Jul 8 15:07:27 CST 2023
filter candidate insertions in high depth region Sat Jul 8 15:07:28 CST 2023
average read number for 200bp bins is 3.2, set read number cutoff to 16
Filtered insertion number: 0 - 0 (overlap rmsk) 0 (short insertion) - 0 (high depth) = 0
/public/home/soft/TEMP2-master/bin/TEMP2_insertion.sh: line 278: Rscript: command not found
generate the overall distribution of transposon mapping reads, first map all reads to transposon Sat Jul 8 15:07:31 CST 2023
sam to bed and bedGraph, multiple mappers are divided by their map times Sat Jul 8 15:07:41 CST 2023
estimate de novo insertion number for each transposon using singleton reads Sat Jul 8 15:08:13 CST 2023
Error: unable to open file or unable to determine types for file test.TPregion.bed

  • Please ensure that your file is TAB delimited (e.g., cat -t FILE).

  • Also ensure that your file has integer chromosome coordinates in the
    expected columns (e.g., cols 2 and 3 for BED).
    Error: unable to open file or unable to determine types for file test.TPregion.bed

  • Please ensure that your file is TAB delimited (e.g., cat -t FILE).

  • Also ensure that your file has integer chromosome coordinates in the
    expected columns (e.g., cols 2 and 3 for BED).
    /usr/bin/env: Rscript: No such file or directory
    generate distribution figures for singleton supporting reads Sat Jul 8 15:08:14 CST 2023
    /usr/bin/env: Rscript: No such file or directory
    filter unreliable singleton insertions, also filter 2p insertions overlapped with similar reference transposon copies Sat Jul 8 15:08:14 CST 2023
    Error: Invalid record in file test.tmp. Record is
    FBgn0000004_17.6 1 0 0 - 0 6 0 0 + 0▒
    Error: Invalid record in file test.tmp. Record is
    FBgn0000004_17.6 1 0 0 - 0 6 0 0 + 0▒
    Calculate frequency of each transposon insertion Sat Jul 8 15:08:14 CST 2023
    get TSD, remove redundant insertions and recalculate de novo insertion rate Sat Jul 8 15:08:17 CST 2023

***** ERROR: Requested column 2, but database file - only has fields 1 - 0.
Error: unable to open file or unable to determine types for file test.TPregion.bed

  • Please ensure that your file is TAB delimited (e.g., cat -t FILE).
  • Also ensure that your file has integer chromosome coordinates in the
    expected columns (e.g., cols 2 and 3 for BED).
    test.t is empty
    calculate de novo insertion rate per genome Sat Jul 8 15:08:18 CST 2023
    clean tmp files Sat Jul 8 15:08:18 CST 2023
    Done, Congras!!!🍺🍺🍺

And the test.insertion.bed file is empty,like this,so how can I solve this problem,thanks.
image

tianxiongbb commented

Hi, this error is because Rscript is not installed in your environment. I should be more specific in the requirements (will rewrite it).