Forum

I have been trying to view the aligned files in the genome browser but I am not able to view the mouse mm10 reference genome. It gives this as the error: Unable to recognize genome reference from the BAM header. Using Human hg19.

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? [enabieva@head02 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 [enabieva@head02 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: [enabieva@head02 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 [enabieva@head02 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

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

How can I upload my private data to the CGC?

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

How do I disable email notifications after job completion?

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 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 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.