Open chetanya opened 9 years ago
chetanya
commented
9 years ago My current environment:
1) zlib/1.2.8 5) gmp/5.1.3 9) star/2.4.1c 13) gsl/1.16 17) torque/4.1.5-test 2) samtools/1.1 6) mpfr/3.1.2 10) velvet/1.1.06 14) geos/3.4.2 18) openmpi/1.6.5 3) bowtie2/2.1.0 7) mpc/1.0.2 11) oases/0.2.09 15) netcdf/4.3.3.1 19) R/3.0.3(default) 4) blat/3.0.5 8) gcc/4.8.2 12) intel/parallel_studio_xe_2015 16) lsf/9.1 20) trup/0.1
chetanya
commented
9 years ago If I understand the code correctly, looks like the "fragment_length.R" script is having issues with the input files. Do you mind looking into this as soon as possible?
ruping
commented
9 years ago Hi, would you mind sending me a small part of your sequencing file (fastq) so I can test it? I have run the pipeline thousands of times without error like that.
simply do "head -400000 fastq_1.fq >sendme_1.fq" and "head -400000 fastq_2.fq >sendme_2.fq"
gzip sendme_1.fq and sendme_2.fq
then send me.
Thanks.
Ruping,
On 7/31/2015 10:41 AM, Chetanya Pandya wrote:
If I understand the code correctly, looks like the "fragment_length.R" script is having issues with the input files. Do you mind looking into this as soon as possible?
— Reply to this email directly or view it on GitHub https://github.com/ruping/TRUP/issues/3#issuecomment-126766697.
^ Sun,Ruping ####################^
@################################@
chetanya
commented
9 years ago Hi Ruping,
You can access the files here: https://drive.google.com/file/d/0B8cD1iIefQ6Bc2V1SVJkbjhrOTA/view?usp=sharing https://drive.google.com/file/d/0B8cD1iIefQ6BenE0Y084VVBXRVU/view?usp=sharing
The commands I'm running: cd /sc/orga/scratch/pandyc01/TRUP
RTrace.pl --runlevel 1 --sampleName sample --seqType p --readpool /sc/orga/scratch/pandyc01/TRUP/Data --root /sc/orga/scratch/pandyc01/TRUP --threads 4 --anno /sc/orga/projects/PBG/REFERENCES/hg19/TRUP/hg19 --QC
RTrace.pl --runlevel 4 --sampleName sample --seqType p --readpool /sc/orga/scratch/pandyc01/TRUP/Data --root /sc/orga/scratch/pandyc01/TRUP --threads 4 --anno /sc/orga/projects/PBG/REFERENCES/hg19/TRUP/hg19 --RA 1
Look forward to hearing from you.
Best, Chetanya
zhaoming159753
commented
9 years ago Hi Ruping, i am using TRUP for RNA-seq analysis and i got the same error with Chetanya.
[2015/8/27 17:37:10] ####### lane name is set to 229a4961-f7eb-44ba-8f63-0021495585e8 #######
lanefile: /lustre/home/medzm/data/TCGA_WGS/TCGA_WGS_RNA-seq/BLCA/229a4961-f7eb-44ba-8f63-0021495585e8/229a4961-f7eb-44ba-8f63-0021495585e8_1.fq.gz lanefile: /lustre/home/medzm/data/TCGA_WGS/TCGA_WGS_RNA-seq/BLCA/229a4961-f7eb-44ba-8f63-0021495585e8/229a4961-f7eb-44ba-8f63-0021495585e8_2.fq.gz
[2015/8/27 17:37:10] ####### preparing directories #######
read length and trimed length are not set, will take the original read length (48 bp) for both (no trimming).
[2015/8/27 17:37:10] ####### runlevel 1 now #######
total number of read pairs: 5329758
[2015/8/27 17:37:15] perl /lustre/home/medzm/software/TRUP-master/bin//spike_in.pl /lustre/home/medzm/data/TCGA_WGS/TCGA_WGS_RNA-seq/TRUP_Pepline/229a4961-f7eb-44ba-8f63-0021495585e8/00_TEST/229a4961-f7eb-44ba-8f63-0021495585e8.spikedin.hits >/lustre/home/medzm/data/TCGA_WGS/TCGA_WGS_RNA-seq/TRUP_Pepline/229a4961-f7eb-44ba-8f63-0021495585e8/00_TEST/229a4961-f7eb-44ba-8f63-0021495585e8.spikedin.fragmentlength
[2015/8/27 17:37:16] ####### runlevel 1 done #######
[2015/8/27 17:37:16] ####### insert mean and sd calculation #######
qual_min: 2; qual_max: 41; qual_zero: 35; qual_shift: -2. Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: read.delim -> read.table Execution halted Use of uninitialized value $number in int at /lustre/home/medzm/software/TRUP-master/bin/RTrace.pl line 2064. Use of uninitialized value $number in numeric ge (>=) at /lustre/home/medzm/software/TRUP-master/bin/RTrace.pl line 2065. Use of uninitialized value $insert_sd in substitution (s///) at /lustre/home/medzm/software/TRUP-master/bin/RTrace.pl line 525. Use of uninitialized value $number in int at /lustre/home/medzm/software/TRUP-master/bin/RTrace.pl line 2064. Use of uninitialized value $number in numeric ge (>=) at /lustre/home/medzm/software/TRUP-master/bin/RTrace.pl line 2065. insert mean: -96 insert_sd: 0 two mates is overlapping too much, please trim more.
what's my problem?
Look forward to hearing from you.
Best Regards;
Ming
Hi,
I would like to use TRUP to detect chimeric fusions in my RNA-Seq datasets. Unfortunately, I keep running into the following issue:
RTrace.pl --runlevel 4 --sampleName sample --seqType p --readpool /sc/orga/scratch/pandyc01/TRUP/Data --root /sc/orga/scratch/pandyc01/TRUP --threads 4 --anno /sc/orga/projects/PBG/REFERENCES/hg19/TRUP/hg19
[2015/6/26 11:1:13] ####### lane name is set to sample #######
lanefile: /sc/orga/scratch/pandyc01/TRUP/Data/sample_R1.fq.gz lanefile: /sc/orga/scratch/pandyc01/TRUP/Data/sample_R2.fq.gz
[2015/6/26 11:1:13] ####### preparing directories #######
read length and trimed length are not set, will take the original read length (100 bp) for both (no trimming).
[2015/6/26 11:1:13] ####### insert mean and sd calculation #######
qual_min: 2; qual_max: 41; qual_zero: 35; qual_shift: -2. Error in setwd(path) : cannot change working directory Execution halted Use of uninitialized value $number in int at /hpc/packages/minerva-common/trup/0.1/TRUP/bin/RTrace.pl line 2064. Use of uninitialized value $number in numeric ge (>=) at /hpc/packages/minerva-common/trup/0.1/TRUP/bin/RTrace.pl line 2065. Use of uninitialized value $insert_sd in substitution (s///) at /hpc/packages/minerva-common/trup/0.1/TRUP/bin/RTrace.pl line 525. Use of uninitialized value $number in int at /hpc/packages/minerva-common/trup/0.1/TRUP/bin/RTrace.pl line 2064. Use of uninitialized value $number in numeric ge (>=) at /hpc/packages/minerva-common/trup/0.1/TRUP/bin/RTrace.pl line 2065. insert mean: -200 insert_sd: 0 two mates is overlapping too much, please trim more.