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LosicLab / starchip

Detection of Circular RNA and Fusions from RNA-Seq
http://starchimp.readthedocs.io/en/latest/
MIT License
32 stars 11 forks source link

always appear those troubles #11

Closed ChrisLou-bioinfo closed 6 years ago

ChrisLou-bioinfo commented 6 years ago

[root@VM_32_17_centos starchip]# ./Step1.sh Filtering out chimeric reads that appear circular Filtering circular reads based on assigned thresholds of 5 reads in 1 individuals Argument "8680r7" isn't numeric in subtraction (-) at /root/starchip/scripts/circles/merge_close_crna_1file.pl line 26, <> line 1588. creating circRNA fasta and gtf for re-alignment and quantification Use of uninitialized value $pos2 in subtraction (-) at /root/starchip/scripts/circles/id2fasta_gtf.pl line 32, line 298. Use of uninitialized value $pos2 in subtraction (-) at /root/starchip/scripts/circles/id2fasta_gtf.pl line 37, line 298. Use of uninitialized value $pos2 in concatenation (.) or string at /root/starchip/scripts/circles/id2fasta_gtf.pl line 39, line 298. Argument "8680r7" isn't numeric in subtraction (-) at /root/starchip/scripts/circles/id2fasta_gtf.pl line 32, line 1455. Argument "chr7" isn't numeric in subtraction (-) at /root/starchip/scripts/c

ChrisLou-bioinfo commented 6 years ago

12hours ago, it works ，why？

kippakers commented 6 years ago

Hi ChrisLou,

I'm trying to sort out what's going wrong for you. Does your most recent comment indicate that STARChip is now running without errors for you? Are your multiple messages about 1 sample, 1 cohort, or many samples, or many cohorts?

In the case above you appear to have just one circRNA that is listed with nonsensical position, "8680r7". Can you search for this string in your file rawdata/cRNA.cutoff.5 and tell me what you find?

Thanks, Kipp