Closed zoe106 closed 3 years ago
I have the same problem.Did you solve it?
Same issue! did you guys managed to solve it?
Did you solve this? Please help me.
It was disc space issue in my case, try to make sure enough space for pipestance pipe line to run
It was disc space issue in my case, try to make sure enough space for pipestance pipe line to run
How large is your disc?
It was disc space issue in my case, try to make sure enough space for pipestance pipe line to run
How large is your disc?
It depends how big is your RNA-seq data to be processed because they’ll be many files to produce by the pipeline. 20G wasn’t enough for me I had to get rid of some stuff
Any update any this? We see the same issue and have ruled out the possibility of insufficient storage.
Job failed in stage code
exit status 255
Waiting 6 seconds for UI to do final refresh.
Pipestance failed.
Use --noexit option to keep UI running after failure.
Hi @twang15 please reach out to support@10xgenomics.com as someone there can help you.
Hi, my command is as followed: nohup time cellranger count --id=SRX6991953 \ --sample=SRX6991953 \ --fastqs=/xtdisk/apod-gen/haoll/xiongyj/1-10X/PRJNA577618/1-output/SRX6991953/ \ --transcriptome=/pnas/zhangz_group/zhangysh/reference/hg38/cellranger/refdata-cellranger-GRCh38-and-mm10-3.1.0/ \ --localcores=32 --noexit \
And I run into an error with "Waiting 6 seconds for UI to do final refresh. Pipestance failed. Use --noexit option to keep UI running after failure." However,when I do put "--noexit", it still not work. Would you please give any suggestion about how to fix it?
############################### Martian Runtime - '3.1.0-v3.2.3' 2020-08-12 15:28:55 [runtime] Reattaching in local mode. Serving UI at http://fat2:37279?auth=BN0YvFY4l8EDcFdkiwphGG0EtiSOWSlPaGbZtVdpMeM
2020-08-12 15:28:58 [runtime] (reset-partial) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk04 2020-08-12 15:28:59 [runtime] (reset-partial) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk05 2020-08-12 15:28:59 [runtime] (reset-partial) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk06 2020-08-12 15:29:00 [runtime] (reset-partial) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk07 2020-08-12 15:29:00 [runtime] (reset-partial) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk08 2020-08-12 15:29:01 [runtime] (reset-partial) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk09 2020-08-12 15:29:01 [runtime] (reset-partial) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk10 2020-08-12 15:29:01 [runtime] (reset-partial) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk11 2020-08-12 15:29:02 [runtime] Found orphaned local stage: ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES 2020-08-12 15:29:02 [runtime] (split_complete) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES 2020-08-12 15:29:02 [runtime] (run:local) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk04.main 2020-08-12 15:29:02 [runtime] (run:local) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk05.main 2020-08-12 15:29:02 [runtime] (run:local) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk06.main 2020-08-12 15:29:02 [runtime] (run:local) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk07.main 2020-08-12 15:29:02 [runtime] (run:local) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk08.main 2020-08-12 15:29:02 [runtime] (run:local) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk09.main 2020-08-12 15:29:02 [runtime] (run:local) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk10.main 2020-08-12 15:29:02 [runtime] (run:local) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES.fork0.chnk11.main 2020-08-12 15:30:01 [runtime] (failed) ID.SRX6991954.SC_RNA_COUNTER_CS.SC_RNA_COUNTER._BASIC_SC_RNA_COUNTER.MARK_DUPLICATES
[error] Pipestance failed. Error log at: SRX6991954/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk06-ud548339a3b/_errors
Log message: thread 'main' panicked at 'Found 0 or >1 features for confidently mapped read/pair 19627721-GTGCCCGT': cr_stage/src/cmd_mark_dups.rs:285stack backtrace: 0: martian::martian_main::{{closure}}::h91b2cb6e4ec208c2 (0x7f3d3018d444) at /mnt/home/jenkins/workspace/cellranger-3.1.0-2.2.5-build/sake/modules/cellranger-cs/3.1.0/lib/rust/.cargo/git/checkouts/martian-rust-35615836cc90309f/56bdd8d/src/lib.rs:418 1: rust_panic_with_hook (0x7f3d3027f0a8) at src/libstd/panicking.rs:482 2: std::panicking::begin_panic::h57e271f882aa496c (0x7f3d30129a69) at /rustc/fc50f328b0353b285421b8ff5d4100966387a997/src/libstd/panicking.rs:412 3: cr_stage::cmd_mark_dups::process_barcode::hd751fc817f7edb3f (0x7f3d301378b9) at cr_stage/src/cmd_mark_dups.rs:285 4: cr_stage::cmd_mark_dups::cmd_mark_dups::hd092a5adfde3f170 (0x7f3d3013d474) at cr_stage/src/cmd_mark_dups.rs:487