Comments (10)
Hi Haynes,
I had a quick look at your data and run the dataset by myself. It seems that your problem was due to the way you run the pipeline. Normally 10X reads have a number of files in a directory and we suggest that the users make a file such as file.dat
q1=/lustre/scratch117/sciops/team117/hpag/zn1/project/mammals/mBosTau1/reads_10x/mBosTau1_S1_L001_R1_001.fastq.gz
q2=/lustre/scratch117/sciops/team117/hpag/zn1/project/mammals/mBosTau1/reads_10x/mBosTau1_S1_L001_R2_001.fastq.gz
q1=/lustre/scratch117/sciops/team117/hpag/zn1/project/mammals/mBosTau1/reads_10x/mBosTau1_S2_L001_R1_001.fastq.gz
q2=/lustre/scratch117/sciops/team117/hpag/zn1/project/mammals/mBosTau1/reads_10x/mBosTau1_S2_L001_R2_001.fastq.gz
q1=/lustre/scratch117/sciops/team117/hpag/zn1/project/mammals/mBosTau1/reads_10x/mBosTau1_S3_L001_R1_001.fastq.gz
q2=/lustre/scratch117/sciops/team117/hpag/zn1/project/mammals/mBosTau1/reads_10x/mBosTau1_S3_L001_R2_001.fastq.gz
q1=/lustre/scratch117/sciops/team117/hpag/zn1/project/mammals/mBosTau1/reads_10x/mBosTau1_S4_L001_R1_001.fastq.gz
q2=/lustre/scratch117/sciops/team117/hpag/zn1/project/mammals/mBosTau1/reads_10x/mBosTau1_S4_L001_R2_001.fastq.gz
You then run the code in this way
scaff10x -nodes 30 {options} -data file.dat funestus_redbean.purged.fa funestus_redbean.scaff10x.fa
You will get a few files
funestus_redbean.scaff10x.fa
funestus_redbean.scaff10x.fa.agp
funestus_redbean.scaff10x.fa.cov
If you use -plot funestus_redbean-bclength.png, you get the barcode length distribution as well.
Another way to run the code is like way you did:
scaff10x -nodes 30 funestus_redbean.purged.fa
bamtofastq_S1_L000_R2_001.fastq.g
bamtofastq_S1_L000_R2_001.fastq.gz
hybrid_redbean2.purged.scaff.fa
However, the file bamtofastq_S1_L000_R1_001.fastq.gz and bamtofastq_S1_L000_R2_001.fastq.gz have to be processed using scaff_reads: barcode tags have been put at the end of the read name. Looks that you didn't do that.
As said before, please use -data file.dat.
Finally, the results of scaf10x are not good, see
/lustre/scratch117/sciops/team117/hpag/zn1/project/worm
A lot of contigs have no read coverage at all. I don't know this is an sample issue or you didn't extract all the reads.
Zemin
from scaff10x.
I wanted to run it this way (.dat file) but got a segfault with that and as the command line usage (when not given any arguments) shows primarily the other way of running, I tried that next. So going back to the .dat way, i still get a segfault.
Segmentation fault scaff10x -nodes 30 -plot barcode_length.png -data scaffinput.dat An_arab_wm_A_ref.fa
in directory /lustre/scratch118/malaria/team222/hh5/projects/analysis/assembly/arabiensis/falcon/haplomerger
from scaff10x.
Your input file
q1=10x_reads/longranger222_wgs_29692_BAdASS7880765_arabiensis_freebayes_LibraryNotSpecified_1_unknown_fc/bamtofastq_S1_L000_bamtofastq_S1_L000_R1_001.fastq.gz
q2=10x_reads/longranger222_wgs_29692_BAdASS7880765_arabiensis_freebayes_LibraryNotSpecified_1_unknown_fc/bamtofastq_S1_L000_bamtofastq_S1_L000_R2_001.fastq.gz
q1=10x_reads/longranger222_wgs_29692_BAdASS7880765_arabiensis_freebayes_LibraryNotSpecified_1_unknown_fc/bamtofastq_S1_L000_bamtofastq_S1_L000_R1_002.fastq.gz
q2=10x_reads/longranger222_wgs_29692_BAdASS7880765_arabiensis_freebayes_LibraryNotSpecified_1_unknown_fc/bamtofastq_S1_L000_bamtofastq_S1_L000_R2_002.fastq.gz
q1=10x_reads/longranger222_wgs_29692_BAdASS7880765_arabiensis_freebayes_LibraryNotSpecified_1_unknown_fc/bamtofastq_S1_L000_bamtofastq_S1_L000_R1_003.fastq.gz
q2=10x_reads/longranger222_wgs_29692_BAdASS7880765_arabiensis_freebayes_LibraryNotSpecified_1_unknown_fc/bamtofastq_S1_L000_bamtofastq_S1_L000_R2_003.fastq.gz
q1=10x_reads/longranger222_wgs_29692_BAdASS7880765_arabiensis_freebayes_LibraryNotSpecified_1_unknown_fc/bamtofastq_S1_L000_bamtofastq_S1_L000_R1_004.fastq.gz
q2=10x_reads/longranger222_wgs_29692_BAdASS7880765_arabiensis_freebayes_LibraryNotSpecified_1_unknown_fc/bamtofastq_S1_L000_bamtofastq_S1_L000_R2_004.fastq.gz
ls -l 10x_reads/longranger222_wgs_29692_BAdASS7880765_arabiensis_freebayes_LibraryNotSpecified_1_unknown_fc/bamtofastq_S1_L000_bamtofastq_S1_L000_R1_001.fastq.gz
ls: cannot access
You need to give the full path.
q1=/lustre/scratch117/sciops/team117/hpag/zn1/project/mammals/mBosTau1/reads_10x/mBosTau1_S1_L001_R1_001.fastq.gz
q2=/lustre/scratch117/sciops/team117/hpag/zn1/project/mammals/mBosTau1/reads_10x/mBosTau1_S1_L001_R2_001.fastq.gz
Zemin
from scaff10x.
I have a debug version for which you can use an existing align.dat file:
/nfs/users/nfs_z/zn1/src/Scaff10X/src/scaff10x -nodes 2 {options} -plot bclength.png -noalign /lustre/scratch117/sciops/team117/hpag/zn1/project/worm/tmp_rununik_57281/align.dat funestus_redbean.purged.fa funestus_redbean.scaff10x-t2.fa > try.out
Note: give the full path of align.dat
Zemin
from scaff10x.
Ok I'm using full paths for all inputs now
./scaffme.sh
File not in the working directory!
File -data not found and please copy it to your working directory!
But it is in the current directory
pwd
/lustre/scratch118/malaria/team222/hh5/projects/analysis/assembly/arabiensis/falcon/haplomerger
(base) haplomerger: ls scaffinput.dat
scaffinput.dat
in scaffme.sh is
cat scaffme.sh
/nfs/users/nfs_s/sm15/dev/Scaff10X-4.1/src/scaff10x -nodes 30 -plot barcode_lengtg.png -data /lustre/scratch118/malaria/team222/hh5/projects/analysis/assembly/arabiensis/falcon/haplomerger/scaffinput.dat /lustre/scratch118/malaria/team222/hh5/projects/analysis/assembly/arabiensis/falcon/haplomerger/An_arab_wm_A_ref.fa
from scaff10x.
Change the scaffme.sh file into this
/nfs/users/nfs_s/sm15/dev/Scaff10X-4.1/src/scaff10x -nodes 30 -plot barcode_lengtg.png -data scaffinput.dat An_arab_wm_A_ref.fa An_arab_wm_A_ref-scaff10x.fa > try.out
from scaff10x.
./scaffme2.sh
(base) haplomerger: cat try.out
File not in the working directory!
File -data not found and please copy it to your working directory!
(base) haplomerger: cat scaffme2.sh
/nfs/users/nfs_s/sm15/dev/Scaff10X-4.1/src/scaff10x -nodes 30 -plot barcode_lengtg.png -data scaffinput.dat An_arab_wm_A_ref.fa An_arab_wm_A_ref-scaff10x.fa > try.out
from scaff10x.
Don't know if Shane has got the recent function for "-plot". Please try to download and install the package for yourself. Or try
/nfs/users/nfs_z/zn1/src/Scaff10X/src/scaff10x
Sorry about all these problems!
from scaff10x.
Just tried
/nfs/users/nfs_z/zn1/src/Scaff10X/src/scaff10x -nodes 52 -plot bclength.png -data file.dat funestus_redbean.purged.fa funestus_redbean.scaff10x-t2.fa >
and Shane's code is working!
from scaff10x.
Ok that seems to be working. Thanks for the help!
from scaff10x.
Related Issues (20)
- No scaffolding being done on the Scaff10xV4 HOT 4
- Segmentation fault HOT 24
- cannot find input.dat HOT 2
- can you update the docs to reflect the actual usage
- run fails at scaff_matrix HOT 8
- another seg fault issue HOT 6
- Floating point exception in break10x HOT 11
- segmentation fault HOT 8
- scaff_reads: Segmentation fault HOT 3
- scaff_bwa segmentation fault HOT 3
- pre n50 = scaff10x n50 HOT 1
- scaff_screeN not found HOT 4
- how does scaff_reads works
- "Numbers of contigs are difference," error in "scaff_bwa-barcode"
- add gnuplot and inkscape to install.sh
- segmentation fault scaff_bwa.c
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from scaff10x.