hi igor,

im trying to run a wes for one sample that was processed by azenta...i uploaded all the required docs for the run and i am getting this error:

[torunp01@bigpurple-ln3 twofortyeight]$ sns/run wes
project dir: /gpfs/data/hackerlab/twofortyeight
code dir: /gpfs/data/hackerlab/twofortyeight/sns
logs dir: /gpfs/data/hackerlab/twofortyeight/logs-sbatch

fix-csv.sh ERROR: file /gpfs/data/hackerlab/twofortyeight/samples.fastq-raw.csv does not exist

when i look at the logs-sbatch it shows: total 0

thank you for your help
pedro

HI All,

I have just run a sns/wes and a little confused of what to do next....
i am in the folder where i see : samples.fastq-raw.csv sns
logs-sbatch samples.fastq-clean.csv settings.txt summary
FASTQ-CLEAN QC-FastQC,

I believe I added the BED file as a reference, but I am not sure..

How would I be able to retrieve these files for generating reports on these different files?

Thank you and sorry for the trouble.

When trying to run the wes-pairs-cnv pipeline, I get the following errors:

logs-qsub/sns.wes-pairs-cnv.SeraCare-1to4-Positive-HapMap-B17-1267.o3950853: get-set-setting.sh ERROR: the value for setting EXP-PROBES-BED must be specified
logs-qsub/sns.wes-pairs-cnv.SeraCare-1to4-Positive-HapMap-B17-1267.o3950853: cnvs-wes-freec.sh ERROR: BED  DOES NOT EXIST

What .bed file is being referenced here and how should it be set?

Good Afternoon,

I am getting this error:

Slurm Job_id=17749799 Name=sns.wes.ptm1__214518 Failed, Run time 00:00:02, FAILED, ExitCode 1

eventhough I have added the reference bed file for the sequence to run...

when I checked the progress or error for the file being run I got this error from terminal, eventhough the reference bed file was copied into the working folder.

align-bwa-mem.sh ERROR: REF DOES NOT EXIST
logs-sbatch/slurm-17749908.out: wes.sh ERROR: SEGMENT align-bwa-mem DID NOT FINISH

Any suggestions?

Thank you

Is it possible to have a route that only runs FastqScreen?

Hi Igor,

How can i define the group that i need to compare to a control (i.e. if i assign the samples as Xmutant and Xwildtype, the results come back comparing Xwildtype to Xmutant) how can i reverse this ? so that i compare Xmutant to Xwildtype ?

Thank you

Good morming Igor,

I have 7 samples 5 normal and two tumor.

The bed file has already bee added and is the same one as I used last time.

-rwx------ 1 torunp01 hackerlab 11302942 Jul 7 12:12 TruSeq_Exome_TargetedRegions_v1.2.bed

Yet I am getting this error:

ogs-sbatch/slurm-18641451.out: get-set-setting.sh ERROR: the value for setting EXP-TARGETS-BED must be specified
logs-sbatch/slurm-18641451.out: qc-target-reads-gatk.sh ERROR: BED DOES NOT EXIST
logs-sbatch/slurm-18641451.out: get-set-setting.sh ERROR: the value for setting EXP-TARGETS-BED must be specified
logs-sbatch/slurm-18641451.out: bam-ra-rc-gatk.sh ERROR: BED DOES NOT EXIST
logs-sbatch/slurm-18641451.out: wes.sh ERROR: SEGMENT bam-ra-rc-gatk DID NOT FINISH
logs-sbatch/slurm-18641452.out: get-set-setting.sh ERROR: the value for setting EXP-TARGETS-BED must be specified

Is there another file I must add?

Thank you
Pedro

Hi, this is not really an issue but more of a question.
For the normalized counts ouput, is it in RPKM?

Hey Igor,

I am doing differential expression analysis on some DNA sequences, and I had some trouble with the sns/run rna-star-groups-dge command as it does not output any r data files or graphs for me to use. Even though I renamed the groups and there were no errors running the run rna-star or the rna-star-groups-dge command, I continuously get an empty r-data folder. Is there anything I can do?

The WES pipeline produces a lot of intermediary files (fastq's, intermediary .bam files, etc) which are not required after the pipeline is finished. They take up a large amount of space, so I think they can probably be deleted (?).

However, if you end up needing those files again, is there an easy way to 'rebuild' those parts of the pipeline output without running the entire pipeline? For example, just run everything ending before the variant calling?

Not sure how easy this would be to implement, or if its already possible without breaking anything. Alternatively, maybe it would be worth having a way to custom-define the segments of a pipeline to be run?

Hi Igor,

Was wondering how can i set assign each group when running rna-star-groups-dge a specific color ?
I have only two groups and I would like to choose which is red and which is blue on the PCA
Thank you

Hello! I'm having a small issue with the ChIP seq peak calling. The first ChIP route worked great. I'm in the same folder and manually edited the samples.pairs.csv with IPs and inputs. I've updated the settings.txt accordingly and I'm still met with :

peaks-macs.sh ERROR: genome dir /gpfs/data/igorlab/ref/hg19
does not exist

I can see I have access to the folder however. Is there a permissions setting? I'm new to this so I'm sure I'm missing something.

Thanks for your time!

The delay between submitting qsub jobs is very slow. Any chance it could be decreased a little? How much delay is really needed?

code is here:

I ran the sns pipeline in one directory, then moved the entire analysis to a different location. When trying to run more pipeline steps after moving, they break with the following error:

logs-qsub/sns.wes-pairs-cnv.Sample1-Sample2.o3950689: wes-pairs-cnv.sh ERROR: BAM /ifs/data/molecpathlab/scripts/snsxt/example_sns_analysis5/BAM-GATK-RA-RC/Sample1.dd.ra.rc.bam DOES NOT EXIST

This is presumably because the directory is no longer located at the path /ifs/data/molecpathlab/scripts/snsxt/example_sns_analysis5, but instead is at a different path (/ifs/data/molecpathlab/NGS580_WES-development/example_sns_analysis_for_validation).

I took a quick look and could not find where the program was getting this original path from, it must be hard-coded somewhere the first time it is run.