Open macmanes opened 4 years ago
Hi Matt,
I have seen anything wrong here for the usage of the code. For any run of scaff10x, it produces a directory such as tmprununik***** to process all the files. Could you tell me the contents in the directory, by doing "ls -lrt"?
Thanks,
Zemin
Sorry I haven't seen anything wrong.
It's empty:
(scaff10x) [macmanes@premise genome]$ ls -lthr tmp_rununik_165217
total 0
@zning-sanger, do you have a small test dataset I could use to make sure this it is not a problem with the installation?
Scratch that. I've identified the bug:
/mnt/lustre/macmaneslab/macmanes/Scaff10X/src/scaff-bin/scaff10x /mnt/lustre/macmaneslab/shared/pero_genomes/Neotomodon_alstoni/genome/Neotomodon_alstoni_10x_v6a.fasta /mnt/lustre/macmaneslab/shared/pero_genomes/Neotomodon_alstoni/reads/NEAL_S1_L006_R1_001.fastq.gz /mnt/lustre/macmaneslab/shared/pero_genomes/Neotomodon_alstoni/reads/NEAL_S1_L006_R2_001.fastq.gz Neotomodon_alstoni_10x_v234.fasta
File not in the working directory!
Input target assembly file1: /mnt/lustre/macmaneslab/shared/pero_genomes/Neotomodon_alstoni/genome/Neotomodon_alstoni_10x_v6a.fasta
File not in the working directory!
Input read1 file: /mnt/lustre/macmaneslab/shared/pero_genomes/Neotomodon_alstoni/reads/NEAL_S1_L006_R1_001.fastq.gz
File not in the working directory!
Input read2 file: /mnt/lustre/macmaneslab/shared/pero_genomes/Neotomodon_alstoni/reads/NEAL_S1_L006_R2_001.fastq.gz
sh: /mnt/lustre/macmaneslab/macmanes/Scaff10X/src/scaff-bin/scaff-bin/scaff_fastq: No such file or directory
Error running command: /mnt/lustre/macmaneslab/macmanes/Scaff10X/src/scaff-bin/scaff-bin/scaff_fastq -name tarseq -len 10 /mnt/lustre/macmaneslab/shared/pero_genomes/Neotomodon_alstoni/genome/Neotomodon_alstoni_10x_v6a.fasta tarseq.fastq tarseq.tag > try.out
See the path for scaff_fastq
? It thinks it's in /mnt/lustre/macmaneslab/macmanes/Scaff10X/src/scaff-bin/scaff-bin/
, there is an "extra" scaff-bin/
in the path. I'm guessing this is not intentional, but I can confirm when I make that directory and copy all the executables in there, that things seem to be working - at least I do not have the same seg fault.
Thanks Mat for the information. I don't know how you installed the package. I just did a test
$ git clone https://github.com/wtsi-hpag/Scaff10X.git $ cd Scaff10X $ ./install.sh
By setting CC= /software/gcc-4.9.2/bin/gcc, it works on the test sample.
Let me know if you have further issues.
Thanks again,
Zemin
sorry..
step 1. binary executes, results in help menu.
step 2. seg fault with dat file
here is the dat file
step 3. segfault with passing reads on the command line