I am currently trying to optimize my 10x chromium de-novo assembly and am trying out different tools to check for assembly errors. The Scaff10x function seems to work perfectly. However, if I try to run the Break10x, I get the following error:
...
[M::mem_pestat] low and high boundaries for proper pairs: (1, 823)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 1535158 reads in 519.780 CPU sec, 20.325 real sec
[main] Version: 0.7.17-r1194-dirty
[main] CMD: /home/user/softwares/scaff10x/Scaff10X/src/scaff-bin/bwa mem -t 30 tarseq.fastq /home/user/my_data/N15_10x/raw_reads/read-BC_1.fastq /home/jderaad/my_data/N15_10x/raw_reads/read-BC_2.fastq
[main] Real time: 234729.355 sec; CPU: 201340.607 sec
sh: /home/user/softwares/scaff10x/Scaff10X/src/scaff-bin/scaff_barcode-length: No such file or directory
sort: cannot read: align.length-5: No such file or directory
There appears to be an error due to the missing "scaff_barcode-length" file and there is no file named "scaff_barcode-length" in the softwares/scaff10x/Scaff10X/src/scaff-bin directory. Is this an error in the script or am I missing a crucial file?
Dear Francesca Giordano,
I am currently trying to optimize my 10x chromium de-novo assembly and am trying out different tools to check for assembly errors. The Scaff10x function seems to work perfectly. However, if I try to run the Break10x, I get the following error:
... [M::mem_pestat] low and high boundaries for proper pairs: (1, 823) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 1535158 reads in 519.780 CPU sec, 20.325 real sec [main] Version: 0.7.17-r1194-dirty [main] CMD: /home/user/softwares/scaff10x/Scaff10X/src/scaff-bin/bwa mem -t 30 tarseq.fastq /home/user/my_data/N15_10x/raw_reads/read-BC_1.fastq /home/jderaad/my_data/N15_10x/raw_reads/read-BC_2.fastq [main] Real time: 234729.355 sec; CPU: 201340.607 sec sh: /home/user/softwares/scaff10x/Scaff10X/src/scaff-bin/scaff_barcode-length: No such file or directory sort: cannot read: align.length-5: No such file or directory
There appears to be an error due to the missing "scaff_barcode-length" file and there is no file named "scaff_barcode-length" in the softwares/scaff10x/Scaff10X/src/scaff-bin directory. Is this an error in the script or am I missing a crucial file?
Kind regards,
Jordi