Ecosyste.ms: Issues

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GitHub / PacificBiosciences/FALCON issues and pull requests

#720 - error "failed multiprocessing" at the step rawreads__tan_apply

Issue - State: closed - Opened by fengli-eGen over 2 years ago - 4 comments

#719 - How to skip repeat mask step?

Issue - State: open - Opened by ttian627 over 2 years ago

#718 - what are the corrected reads?

Pull Request - State: open - Opened by ttian627 over 2 years ago

#717 - FALCON ERROR: FC_RUN.CFG

Issue - State: closed - Opened by rokalca almost 3 years ago

#716 - Falcon unzip mechanisms

Issue - State: open - Opened by mentorlg over 3 years ago

#715 - Available input for Falcon-Unzip

Issue - State: closed - Opened by mentorlg over 3 years ago - 1 comment

#714 - Hi , i meet the error : Task Node(0-rawreads/build) failed with exit-code=1

Issue - State: closed - Opened by lsj11211 over 3 years ago - 3 comments

#713 - Unable to run my PacBio data with snakemake and pbassembly

Issue - State: closed - Opened by wjj666 over 3 years ago - 1 comment

#712 - quiver-run failed at variantCaller

Issue - State: closed - Opened by yanboANU over 3 years ago - 1 comment

#710 - Failed to parse config "fc_run.cfg"

Issue - State: closed - Opened by linshengnan2020 about 4 years ago - 1 comment

#709 - [ERROR]Task Node(0-rawreads/build) failed with exit-code=256

Issue - State: closed - Opened by cwarden45 about 4 years ago - 21 comments

#707 - Assembly with example data on slurm failed: {Node(0-rawreads/build)}

Issue - State: closed - Opened by sadikmu over 4 years ago - 6 comments

#706 - LAmerge: System error, read failed!

Issue - State: open - Opened by cassondranewman over 4 years ago - 1 comment

#705 - Is preads4falcon.fasta the error corrected reads?

Issue - State: closed - Opened by aboyher over 4 years ago - 9 comments

#704 - questions about speed and ONT reads

Issue - State: open - Opened by mycecilia over 4 years ago

#703 - problems while 2-asm-falcon

Issue - State: closed - Opened by X-WJ almost 5 years ago - 3 comments

#702 - FALCON on PBSPro 0-rawreads/tan-runs/tan_003 fails with datander error

Issue - State: open - Opened by bifxcore almost 5 years ago - 1 comment

#701 - pb-assembly fails at 2-asm-falcon stage with unclear error

Issue - State: closed - Opened by charlesfeigin about 5 years ago - 2 comments

#700 - Running Test cfg fails

Issue - State: closed - Opened by KarlFetter about 5 years ago - 1 comment

#699 - Quiver-chunks not completing

Issue - State: closed - Opened by nicolasalexandre21 about 5 years ago - 3 comments

#698 - [falcon-unzip] ctg_list file generated, but nothing in the file

Issue - State: closed - Opened by KyuKyu-dplearn about 5 years ago - 2 comments

#697 - [ERROR]Task Node(2-asm-falcon) failed with exit-code=1

Issue - State: closed - Opened by liufeibio about 5 years ago - 3 comments

#696 - fc_unzip.py run error

Issue - State: closed - Opened by wuxiaopei0509 about 5 years ago - 1 comment

#695 - Unable to run my PacBio data

Issue - State: closed - Opened by crkmary about 5 years ago - 1 comment

#694 - falcon-unzip error :Call 'which gcpp' returned 256

Issue - State: closed - Opened by wuxiaopei0509 about 5 years ago - 1 comment

#693 - FALCON runs, Unzip doesn't, but I can't find the error

Issue - State: closed - Opened by michaeljmetzger about 5 years ago - 12 comments

#692 - Job Failure Initial Steps

Issue - State: closed - Opened by mbcouger about 5 years ago - 2 comments

#691 - SLURM parameters to submit falcon assembly

Issue - State: closed - Opened by scauet over 5 years ago - 3 comments

#690 - How to modify configure file to specify RAM and CPU number

Issue - State: closed - Opened by feixue1039 over 5 years ago - 1 comment

#689 - running falon.unzip is wrong

Issue - State: closed - Opened by wuxiaopei0509 over 5 years ago - 3 comments
Labels: duplicate

#688 - pkg_resources.DistributionNotFound

Issue - State: closed - Opened by wuxiaopei0509 over 5 years ago - 1 comment

#687 - Exception: Call '/bin/bash user_script.sh' returned 256.

Issue - State: closed - Opened by llengcn over 5 years ago - 2 comments

#686 - Failed to set up logging / MissingSectionHeaderError

Issue - State: open - Opened by AlBaarS over 5 years ago - 1 comment

#685 - [ERROR]Task Node(0-rawreads/build) failed with exit-code=1

Issue - State: closed - Opened by nicolasalexandre21 over 5 years ago - 3 comments

#684 - overlap between contigs

Issue - State: open - Opened by wawjcwxy almost 6 years ago

#683 - poor result and preassembled_yield

Issue - State: closed - Opened by ptranvan almost 6 years ago - 2 comments

#682 - Meaning of gfa outputs

Issue - State: closed - Opened by gbdias almost 6 years ago - 2 comments
Labels: question

#681 - Problem of Python version on cluster

Issue - State: closed - Opened by Lcornet almost 6 years ago

#680 - subjobs pending status Eqw

Issue - State: closed - Opened by Lcornet almost 6 years ago - 1 comment

#678 - ERROR:ailed to kill job for heartbeat (which might mean it was already gone)

Issue - State: closed - Opened by Hongchang-Gu almost 6 years ago - 7 comments

#677 - Task Node(0-rawreads/tan-runs/tan_005) failed with exit-code=1

Issue - State: closed - Opened by amnag almost 6 years ago - 2 comments

#676 - daligner: time estimates

Issue - State: closed - Opened by aechchiki about 6 years ago

#675 - falcon_unzip result

Issue - State: closed - Opened by lijingjing1 about 6 years ago - 1 comment

#673 - Make build and dust job step configurable

Pull Request - State: closed - Opened by mp15 about 6 years ago - 3 comments

#672 - pytest failures

Issue - State: closed - Opened by mestia about 6 years ago - 5 comments

#671 - Can't start assembly jobs for the latest version of falcon

Issue - State: closed - Opened by fayina about 6 years ago - 1 comment

#670 - 2018.08.31 binaries LAcheck duplicate in tan-runs

Issue - State: closed - Opened by jasmynp about 6 years ago - 6 comments

#669 - falcon_kit.mains.ovlp_to_graph fails to produce c_path files

Issue - State: closed - Opened by fayina about 6 years ago - 3 comments

#668 - daligner_p Segmentation fault

Issue - State: closed - Opened by xinwang-bio about 6 years ago - 2 comments

#667 - Cluster renting

Issue - State: open - Opened by mictadlo about 6 years ago

#666 - tan-runs cannot find build/raw_reads.db under tan-chunks

Issue - State: closed - Opened by jasmynp about 6 years ago - 4 comments

#665 - Error correction with Illumina

Issue - State: open - Opened by mictadlo about 6 years ago - 2 comments

#664 - help with SLURM config for fs_based, sbatch

Issue - State: closed - Opened by jasmynp over 6 years ago - 14 comments

#663 - Running Falcon locally, with large genomes

Issue - State: closed - Opened by bernardo1963 over 6 years ago - 7 comments

#662 - MissingLas: 76728 is not a perfect square. We must be missing some .las files.

Issue - State: closed - Opened by roylejw over 6 years ago - 1 comment

#661 - Unable to complete Falcon test run: fc_run fails to parse config file

Issue - State: closed - Opened by ggstatgen over 6 years ago - 2 comments

#659 - Regarding Filtering Synthetic construct PacBio

Issue - State: closed - Opened by harsh-shukla over 6 years ago - 2 comments

#658 - Examples of up-to-date cfg files for FALCON?

Issue - State: closed - Opened by apredeus over 6 years ago - 22 comments

#657 - Error running Falcon unzip

Issue - State: closed - Opened by ghannum over 6 years ago - 1 comment

#656 - Using PacBio and Nanopore data together?

Issue - State: closed - Opened by apredeus over 6 years ago - 1 comment

#655 - issue with slurm

Issue - State: closed - Opened by fmarletaz over 6 years ago - 2 comments

#654 - Estimation of free disc space needed?

Issue - State: closed - Opened by alslonik over 6 years ago - 1 comment

#653 - Problem with restarting

Issue - State: closed - Opened by gengyuncong over 6 years ago - 1 comment

#652 - Assertion error running Falcon unzip

Issue - State: closed - Opened by ghannum over 6 years ago - 2 comments

#651 - How to set tmpDir of pbalign when running fc_quiver

Issue - State: open - Opened by pwmcclurg over 6 years ago - 2 comments

#650 - falcon_unzip failed at 3-unzip/2-htigs/chunk_000***F

Issue - State: closed - Opened by whc2 over 6 years ago - 3 comments

#649 - Falcon vs Falcon-integrate

Issue - State: closed - Opened by alslonik over 6 years ago - 1 comment

#648 - number of concurrent jobs fixed to 8

Issue - State: closed - Opened by gengyuncong over 6 years ago - 2 comments

#640 - too many arguments for format string

Pull Request - State: open - Opened by peterjc over 6 years ago - 4 comments

#639 - Large genomes

Issue - State: closed - Opened by iggyB over 6 years ago - 1 comment
Labels: question

#637 - Unclear release information

Issue - State: closed - Opened by peterjc over 6 years ago - 3 comments

#636 - missing reads.fa files during unzip

Issue - State: closed - Opened by rob123king over 6 years ago - 5 comments

#635 - high heterozygous genome

Issue - State: closed - Opened by yplee614 over 6 years ago - 3 comments

#632 - Problems with trying to assemble corrected sequences in FALCON

Issue - State: closed - Opened by ruthfa over 6 years ago - 19 comments

#631 - Some 0-rawreads jobs failing with ERROR 256 and "Too many alignment records"

Issue - State: closed - Opened by cschu over 6 years ago - 1 comment

#630 - Task Node(0-rawreads) failed with exit-code=256

Issue - State: closed - Opened by AlexYang01 over 6 years ago - 1 comment

#628 - What to put into input.fofn for FALCON-unzip

Issue - State: closed - Opened by LukeManship over 6 years ago - 2 comments

#627 - setting tmpdir

Issue - State: closed - Opened by rob123king over 6 years ago - 1 comment

#626 - `get_cns_from_align_tags` may lose the first base in falcon.c:519 (@05ed6fa)

Issue - State: closed - Opened by lemene over 6 years ago - 4 comments

#624 - "g_best_ck" may be misused in falcon.c:494 (@09a8b7b)

Issue - State: closed - Opened by lemene over 6 years ago - 5 comments
Labels: bug

#622 - use FALCON in PBS grid

Issue - State: closed - Opened by tangerzhang over 6 years ago - 3 comments

#603 - Running Falcon assembly steps manually

Issue - State: closed - Opened by mictadlo almost 7 years ago - 9 comments

#590 - Falcon assembly question

Issue - State: closed - Opened by yuragal about 7 years ago - 2 comments

#588 - lfs setstripe -c 12 ?

Issue - State: closed - Opened by amiably about 7 years ago - 5 comments

#569 - identification of segmental duplication from contigs

Issue - State: closed - Opened by madhubioinfo over 7 years ago - 2 comments

#546 - if change config file and restart falcon, old config parameters continue to be used. why?

Issue - State: closed - Opened by dgordon562 over 7 years ago - 19 comments
Labels: question

#525 - Running FALCON using PBS

Issue - State: closed - Opened by MarisaMiller almost 8 years ago - 10 comments

#514 - falcon overlap filtering settings for humans

Issue - State: closed - Opened by sjin09 almost 8 years ago - 11 comments
Labels: question

#507 - unknown reason failed after the program steped into '1-preads-ovl' and can't resume

Issue - State: closed - Opened by nottwy almost 8 years ago - 17 comments

#501 - Re-running FALCON for unsatisfied jobs

Issue - State: closed - Opened by sjin09 almost 8 years ago - 16 comments

#456 - Unable to run Falcon

Issue - State: closed - Opened by agroppi about 8 years ago - 3 comments

#254 - Do not exit on daligner failure

Pull Request - State: closed - Opened by pb-cdunn almost 9 years ago

#99 - Proper ext_modules; Travis CI

Pull Request - State: closed - Opened by pb-cdunn over 9 years ago - 2 comments