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plot DNA feature error #85

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yangfeizZZ opened this issue Jul 1, 2023 · 0 comments
Open

plot DNA feature error #85

yangfeizZZ opened this issue Jul 1, 2023 · 0 comments

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@yangfeizZZ
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I have a GTF file. When i use coolbox to draw the DNA duture with GTF file on jupyter notebook, i occured an error :
CalledProcessError: Command '['tabix', '-p', 'gff', '../../reference/huangniu/GCF_002263795.1_ARS-UCD1.2_genomic.gtf.bgz']' returned non-zero exit status 1.

Then i run "tabix -p gff ../../reference/huangniu/GCF_002263795.1_ARS-UCD1.2_genomic.gtf.bgz',it also occured an error:
[E::hts_idx_push] Unsorted positions on sequence #2: 148410857 followed by 66847172

When i open the *.gtf.bgz, i found it not sort in some lines, such as
微信截图_20230630230504

Then i run "grep -v ^"#" GCF_002263795.1_ARS-UCD1.2_genomic_filter.gtf | sort -t$'\t' -k1,1 -k4,4n", the result is true:
微信截图_20230630231659

Finally, coolbox is working.

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