Closed JunmingH closed 4 years ago
Hi @JunmingH,
you would have to combing the different output files, into one set of files with multiple columns for each of the samples. However, the rows will be different, too, since not all circRNAs will be detect in each sample. I would recommend to try to get all sample processed by DCC in one run, possibly with -T 2 or 2 to not create too much CPU and memory load.
Cheers, Tobias
Hi @tjakobi Tobias,
I was trying to using server to processing the data but still gave me the error,
Traceback (most recent call last):
File "/restricted/projectnb/casa/jmh/RNA-seq/circu_RNA/DCC-0.4.7/DCC/main.py", line 818, in
Could you please attach the log file of that DCC run?
samplesheet.txt bam_files.txt DDC2_e.txt DDC2_o.txt Attached is
@tjakobi Can you give me some idea for this?
Hi @JunmingH,
I am relatively sure that your command line is not correct, see the following error:
DDC2_o.txt: => locating circRNAs (unstranded mode) [/restricted/projectnb/casa/jmh/RNA-seq/circu_RNA/script/samplesheet]
DDC2_o.txt:WARNING: File /restricted/projectnb/casa/jmh/RNA-seq/circu_RNA/script/samplesheet, line 2 does not contain all features.
DDC2_o.txt:WARNING: /restricted/projectnb/casa/jmh/RNA-seq/circu_RNA/script/samplesheet is probably corrupt.
Here the Junctions files should be scanned, not the samplesheet.
Can you please provide your complete command line?
Cheers, Tobias
@tjakobi Hi Tobias,
Attached is~ python2 ${app_dir}/main.py @samplesheet -D -N -R ${gtf_dir}/GRCh38_Repeats_simpleRepeats_RepeatMasker.gtf -an ref/GRCh38/annotation/Homo_sapiens.GRCh38.95.gtf -F -M -Nr 1 1 -fg -G -A ref/Homo_sapiens.GRCh38.dna.primary_assembly.fa -T 2 -O /dcc_all_results/ -B @bam_files
The samplesheet and the command line look okay - however DCC seems to think there is only one input file called samplesheet.
Your command line is not the command line that DCC itself prints out, do you have the complete DCC log, i.e. DCC-2019***.log
? That log file contains the actuall command line DCC sees.
Cheers, Tobias
@tjakobi Sure, Attached is 2019-11-24 14:54:23,207 DCC 0.4.7 started 2019-11-24 14:54:23,207 DCC command line: /jmh/RNA-seq/circu_RNA/DCC-0.4.7/DCC/main.py /jmh/RNA-seq/circu_RNA/script/samplesheet -D -N -R jmh/RNA-seq/circu_RNA/script/ref/GRCh38_Repeats_simpleRepeats_RepeatMasker.gtf -an /jmh/ref/GRCh38/annotation/Homo_sapiens.GRCh38.95.gtf -F -M -Nr 1 1 -fg -G -A /bu_brain_rnaseq/hjm_test/step_by_step/ref_RSEM/ref/Homo_sapiens.GRCh38.dna.primary_assembly.fa -T 2 -O /jmh/RNA-seq/circu_RNA/dcc_all_results/ -B /jmh/RNA-seq/circu_RNA/script/bam_files 2019-11-24 14:54:23,422 Starting to detect circRNAs 2019-11-24 14:54:23,422 Non-stranded data, the strand of circRNAs guessed from the strand of host genes 2019-11-24 14:54:23,423 started circRNA detection from file /jmh/RNA-seq/circu_RNA/script/samplesheet
Hi @JunmingH,
from the log file you can see that the actual command line is
jmh/RNA-seq/circu_RNA/DCC-0.4.7/DCC/main.py /jmh/RNA-seq/circu_RNA/script/samplesheet
While it should be
jmh/RNA-seq/circu_RNA/DCC-0.4.7/DCC/main.py @/jmh/RNA-seq/circu_RNA/script/samplesheet
The @ for the input is missing.
Cheers, Tobias
Hi @tjakobi Tobias
Thanks for your help! It's working right now!
Hi I was trying to combine the results together. since there have have issue when I integrate those bam files together. Right now I have CircCoordinates CircRNACount CircSkipJunctions LinearCount Four files for each subjects. I was wondering how could I cimbine each subjects together. using which column to match them? Thanks!