Hi CGC Team, I am planning to use the tissue slides and the gene expression data from TCGA. Therefore I need the connections between the two units. Since the TCGA barcodes sometimes don't match (e.g. if the portion number is different), I want to use the metadata to get this information. I created the query for it and tried to download the connections. But if I export the corresponding file, I can only download up to 3000 lines. That would be enough, but if I drop all duplicates, I only have 100 lines. Is there a way to download the hole table directly from the query? Best regards, Lena

Hi! I am analyzing the TCGA MAF files using terminal in Data cruncher. Some MAF files are .gz format and I have to unzip them. But it's a read-only file system. Would you please help find a solution? Thank you! Best, Yiyun

Hi, I'm doing somatic mutation calling of a TCGA patient TCGA-AR-A1AO and am using the BAM file in databrower. I'm using the BAM files TCGA-AR-A1AO-10A-01D-A12Q-09_IlluminaGA-DNASeq_exome_gdc_realn.bam uuid:30f1d9e3-e6a5-44b6-846c-1497806d301c size: 27.03GB TCGA-AR-A1AO-01A-01D-A12Q-09_IlluminaGA-DNASeq_exome_gdc_realn.bam uuid: 33eeb804-ca8b-491e-8221-a285743be692 size: 25.53GB However, on GDC portal, the files are 29.02GB and 27.41GB respectively. I wonder if those files are really up to date as the file sizes are different and my somatic mutation calling result using Varscan2 is missing variants comparing to GDC results(Under same parameters and inputs.) It is just confusing so I am troubleshooting right now. Woule you please help me on this? Thanks! Best, Stella

Hi, I'm using STAR genome generate and STAR from public apps (both 2.7.0e) to align a human RNA-seq data (uploaded privately) and I'm using GRCh38.primary_assembly.genome.fa and gencode.v32.annotation.gtf as the reference genome and gene annotation file for genome indices generation. I keep getting this error: Command mkdir genomeDir && STAR --runMode genomeGenerate --genomeDir ./genomeDir --runThreadN 20 --genomeChrBinNbits 16 --limitGenomeGenerateRAM 60000000000 --genomeFastaFiles /sbgenomics/workspaces/2bc67190-cbb2-43ba-866b-ca9e77ce024a/tasks/a72a496a-3859-480c-8de1-31c0e332b50e/star_genome_generate_2_7_0e/GRCh38.primary_assembly.genome.fa --sjdbGTFfile /sbgenomics/workspaces/2bc67190-cbb2-43ba-866b-ca9e77ce024a/tasks/a72a496a-3859-480c-8de1-31c0e332b50e/star_genome_generate_2_7_0e/gencode.v32.annotation.gtf && tar -vcf GRCh38.primary_assembly.genome.gencode.v32.annotation.star-2.7.0e-index-archive.tar ./genomeDir && mv Log.out Log.out.log failed with exit code 137. Can someone tell me how to solve this? Thank you!

Hi! I am recently using the Varscan2 workflow from BAM to do somatic mutation calling of TCGA GRch38 BAM files. However, the output high confidence vcf files is only a few kb large. One of the patient I was looking, TCGA-AR-A1AO has around 6000 mutations called in the MuTect vcf but only have 300 mutations in my output. I didn't change any parameters. I wonder if it's the problem of input files but I was just using the tumor-normal bam in TCGA.

I've set up a Volume to access files from a bucket I have under my own AWS account and copied a file into a project. Does this copy incur storage charges of its own?

Hi, I want to know how to pull image from CGC repository. Taken STAR as an example, I had tried to use "docker run -ti cgc-images.sbgenomics.com/admin/sbg-public-data/rna-seq-alignment-star-2-5-4b", but it didn't work. Can anyone tell me how to do, thanks in advance!

How do I disable email notifications after job completion?

LUAD clinical data has a parameter paper_iCluster.Group. What does it stand for, I can't find the definition anywhere

Greetings. I was wondering if you could help me. I have a number of files in a project that I am on that I would like to copy to an Amazon S3 bucket. I have mounted the bucket on a volume. However, it is not clear how to copy the files to the bucket. While https://docs.cancergenomicscloud.org/docs/aws-cloud-storage-tutorial#move-file-from-project shows how to move a particular file, I would like to move many files. Is this something that can be done via the Cancer Genomics Cloud GUI/web interface, or is there is some link showing me how it can be done? Many thanks!

How can I upload my private data to the CGC?

For 3 days now, when I enter the ICGC Data Portal I get the error: "This site can’t be reached" Anyone know what the problem is? Is there another way to enter the portal? Thanks

Hi, I'm trying to download a SGDP file via wget and the download link. I get error 403. Could you please explain the nature of the error? [[email protected] sgdp]$ wget https://sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com/cgl-sgdd-reorg/SGDP/REMAP_hs37d5/LP6005441-DNA_A01.annotated.nh.vcf.gz?x-username=enabieva&x-env=cgc&x-requestId=f1d09f8c-754d-4a6b-b2c8-d252cd81e390&x-project=sevenbridges%2Fsimons-genome-diversity-project-sgdp&response-content-disposition=attachment%3Bfilename%3DLP6005441-DNA_A01.annotated.nh.vcf.gz&response-content-type=application%2Foctet-stream&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20220323T140118Z&X-Amz-SignedHeaders=host&X-Amz-Expires=172799&X-Amz-Credential=AKIAJQD4ZMI5SNVG2A2A%2F20220323%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=96f71ce17b3a206fce4fd77c116a7f81ce85e53de78467c016b61ebb4d6cf4c5 [2] 9275 [3] 9276 [4] 9277 [5] 9279 [6] 9280 -bash: x-env=cgc: co mmand not found [7] 9281 -bash: x-requestId=f1d09f8c-754d-4a6b-b2c8-d252cd81e390: command not found [8] 9282 -bash: x-project=sevenbridges%2Fsimons-genome-diversity-project-sgdp: command not found -bash: response-content-disposition=attachment%3Bfilename%3DLP6005441-DNA_A01.annotated.nh.vcf.gz: command not found [9] 9283 -bash: response-content-type=application%2Foctet-stream: command not found -bash: X-Amz-Algorithm=AWS4-HMAC-SHA256: command not found [10] 9284 [11] 9285 -bash: X-Amz-Date=20220323T140118Z: command not found -bash: X-Amz-SignedHeaders=host: command not found [12] 9286 -bash: X-Amz-Expires=172799: command not found -bash: X-Amz-Credential=AKIAJQD4ZMI5SNVG2A2A%2F20220323%2Fus-east-1%2Fs3%2Faws4_request: command not found --2022-03-23 17:41:00-- https://sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com/cgl-sgdd-reorg/SGDP/REMAP_hs37d5/LP6005441-DNA_A01.annotated.nh.vcf.gz?x-username=enabieva -bash: X-Amz-Signature=96f71ce17b3a206fce4fd77c116a7f81ce85e53de78467c016b61ebb4d6cf4c5: command not found [3] Exit 127 x-env=cgc [4] Exit 127 x-requestId=f1d09f8c-754d-4a6b-b2c8-d252cd81e390 [5] Exit 127 x-project=sevenbridges%2Fsimons-genome-diversity-project-sgdp [6] Exit 127 response-content-disposition=attachment%3Bfilename%3DLP6005441-DNA_A01.annotated.nh.vcf.gz [7] Exit 127 response-content-type=application%2Foctet-stream [8] Exit 127 X-Amz-Algorithm=AWS4-HMAC-SHA256 [9] Exit 127 X-Amz-Date=20220323T140118Z [10] Exit 127 X-Amz-SignedHeaders=host [11] Exit 127 X-Amz-Expires=172799 [12]- Exit 127 X-Amz-Credential=AKIAJQD4ZMI5SNVG2A2A%2F20220323%2Fus-east-1%2Fs3%2Faws4_request [[email protected] sgdp]$ Resolving sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com... 52.217.94.241 Connecting to sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com|52.217.94.241|:443... connected. HTTP request sent, awaiting response... 403 Forbidden 2022-03-23 17:41:01 ERROR 403: Forbidden. [2]- Exit 8 wget https://sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com/cgl-sgdd-reorg/SGDP/REMAP_hs37d5/LP6005441-DNA_A01.annotated.nh.vcf.gz?x-username=enabieva

Hi, I'm trying to download a SGDP file via wget and the download link. I get error 403: [[email protected] sgdp]$ wget https://sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com/cgl-sgdd-reorg/SGDP/REMAP_hs37d5/LP6005441-DNA_A01.annotated.nh.vcf.gz?x-username=enabieva&x-env=cgc&x-requestId=f1d09f8c-754d-4a6b-b2c8-d252cd81e390&x-project=sevenbridges%2Fsimons-genome-diversity-project-sgdp&response-content-disposition=attachment%3Bfilename%3DLP6005441-DNA_A01.annotated.nh.vcf.gz&response-content-type=application%2Foctet-stream&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20220323T140118Z&X-Amz-SignedHeaders=host&X-Amz-Expires=172799&X-Amz-Credential=AKIAJQD4ZMI5SNVG2A2A%2F20220323%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=96f71ce17b3a206fce4fd77c116a7f81ce85e53de78467c016b61ebb4d6cf4c5 [2] 9275 [3] 9276 [4] 9277 [5] 9279 [6] 9280 -bash: x-env=cgc: co mmand not found [7] 9281 -bash: x-requestId=f1d09f8c-754d-4a6b-b2c8-d252cd81e390: command not found [8] 9282 -bash: x-project=sevenbridges%2Fsimons-genome-diversity-project-sgdp: command not found -bash: response-content-disposition=attachment%3Bfilename%3DLP6005441-DNA_A01.annotated.nh.vcf.gz: command not found [9] 9283 -bash: response-content-type=application%2Foctet-stream: command not found -bash: X-Amz-Algorithm=AWS4-HMAC-SHA256: command not found [10] 9284 [11] 9285 -bash: X-Amz-Date=20220323T140118Z: command not found -bash: X-Amz-SignedHeaders=host: command not found [12] 9286 -bash: X-Amz-Expires=172799: command not found -bash: X-Amz-Credential=AKIAJQD4ZMI5SNVG2A2A%2F20220323%2Fus-east-1%2Fs3%2Faws4_request: command not found --2022-03-23 17:41:00-- https://sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com/cgl-sgdd-reorg/SGDP/REMAP_hs37d5/LP6005441-DNA_A01.annotated.nh.vcf.gz?x-username=enabieva -bash: X-Amz-Signature=96f71ce17b3a206fce4fd77c116a7f81ce85e53de78467c016b61ebb4d6cf4c5: command not found [3] Exit 127 x-env=cgc [4] Exit 127 x-requestId=f1d09f8c-754d-4a6b-b2c8-d252cd81e390 [5] Exit 127 x-project=sevenbridges%2Fsimons-genome-diversity-project-sgdp [6] Exit 127 response-content-disposition=attachment%3Bfilename%3DLP6005441-DNA_A01.annotated.nh.vcf.gz [7] Exit 127 response-content-type=application%2Foctet-stream [8] Exit 127 X-Amz-Algorithm=AWS4-HMAC-SHA256 [9] Exit 127 X-Amz-Date=20220323T140118Z [10] Exit 127 X-Amz-SignedHeaders=host [11] Exit 127 X-Amz-Expires=172799 [12]- Exit 127 X-Amz-Credential=AKIAJQD4ZMI5SNVG2A2A%2F20220323%2Fus-east-1%2Fs3%2Faws4_request [[email protected] sgdp]$ Resolving sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com... 52.217.94.241 Connecting to sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com|52.217.94.241|:443... connected. HTTP request sent, awaiting response... 403 Forbidden 2022-03-23 17:41:01 ERROR 403: Forbidden. [2]- Exit 8 wget https://sb-datasets-us-east-1.s3-fips.us-east-1.amazonaws.com/cgl-sgdd-reorg/SGDP/REMAP_hs37d5/LP6005441-DNA_A01.annotated.nh.vcf.gz?x-username=enabieva