PacificBiosciences FALCON_unzip issues

PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study

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issues

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location of Haplotigs on Primary contigs and read alignment to both

#70 conte1 opened 7 years ago
2
Best way to quantify / check the changes unzip does to the assembly

#69 roblehmann closed 7 years ago
1
unable to find smrtsuit3.0 for Falcon-unzip

#68 amit4mchiba closed 7 years ago
1
updated falcon-unzip not reading cfg file correctly

#67 mahulchak closed 7 years ago
4
fc_quiver.py does not get past quiver_scatter

#66 kevlim83 closed 7 years ago
10
fail to open a sam file

#65 IEkAdN opened 7 years ago
3
all_p_ctg.fa file with empty sequences

#64 kevlim83 opened 7 years ago
0
falcon_kit.mains.rr_ctg_track causing a lot of paging

#63 msc51 closed 7 years ago
1
falcon_unzip error using ./unzip.sh

#62 shilpagarg closed 7 years ago
18
getting errors in run_quiver.py step in falcon_unzip

#61 bostanict closed 7 years ago
8
Proposed fix for cigarString issues

#60 mhsieh closed 7 years ago
1
Avoid long ref_seq string in parameters for falcon_unzip.phasing.make_het_call

#59 pb-cdunn closed 7 years ago
0
FALCON_unzip reverts to job_type=local

#58 roblehmann closed 7 years ago
2
Problem to run last version of falcon-unzip

#57 a-velt closed 7 years ago
28
python -m not finding function for get_read_ctg_map

#56 YourePrettyGood closed 7 years ago
7
samtobed.py - unforgiving license terms

#55 0xaf1f closed 7 years ago
2
Choose unzip_concurrent_jobs and quiver_concurrent_jobs parameters.

#54 a-velt closed 7 years ago
5
Resuming falcon_unzip from specific step

#53 bostanict opened 7 years ago
5
blasr 5.3.56ec927 with current FALCON_UNZIP fails in quiver: "read group ID not found"

#52 roblehmann closed 7 years ago
8
Running falcon_unzip error: "[ERROR]Contents of '/data1/ls2017/falcon/tests/unzip/run1119/./3-unzip/0-phasing/000000F/p_000000F.sh.log':"

#51 ls2017 closed 7 years ago
6
20161111|121503| 46693| ERROR: mummer and/or mgaps returned non-zero

#50 danshu closed 7 years ago
1
Running falcon_unzip error: "ImportError: No module named falcon_kit"

#49 ls2017 closed 7 years ago
2
[E::hts_open_format] fail to open file '../4-quiver/reads/000011F_036.sam

#48 danshu closed 7 years ago
7
Falcon Unzip documentation

#47 yingzhang121 closed 7 years ago
1
from: can't read /var/mail/falcon_unzip.ovlp_filter_with_phase

#46 danshu closed 7 years ago
7
Binary package for Bioconda

#45 mictadlo opened 8 years ago
1
Failed to recurse into submodule path 'FALCON'

#44 mictadlo closed 8 years ago
8
fatal: unable to checkout working tree

#43 mictadlo closed 8 years ago
4
Empty FALCON folder

#42 mictadlo closed 8 years ago
3
Compatibility question

#41 mahulchak closed 7 years ago
6
FileNotExistError: "No such file:'/data/falcon/0-rawreads/raw_reads.db' on '......'"

#40 danshu closed 7 years ago
6
Assembling telomeres

#39 KSchnee opened 8 years ago
0
Sharing scripts for generating Figure3 in FALCON-Unzip preprint.

#38 JinfengChen closed 8 years ago
6
task "hasm.sh-hasm-hasm" took very long time

#37 ghost closed 8 years ago
3
How to run SMRT-analysis?

#36 ls2017 closed 8 years ago
5
Version question

#35 ebioman closed 8 years ago
2
Possible mummer issue during hasm.sh

#34 peterdfields closed 7 years ago
28
use falcon-unzip for tetraploid

#33 tangerzhang opened 8 years ago
1
missing primary contigs after cns

#32 skingan closed 8 years ago
2
Quiver step failing since it can not find some files to delete

#31 ghost closed 8 years ago
11
BAM file necessary for quiver step?

#30 ghost closed 8 years ago
2
blasr 5.2 fundamentally incompatible with current FALCON_UNZIP?

#29 ghost opened 8 years ago
27
task_hasm() dies on missing ctgs

#28 flowers9 closed 7 years ago
2
wait_for_file and nfs file systems

#27 flowers9 closed 7 years ago
1
poor shutdown/restart handling with partially written files

#26 flowers9 opened 8 years ago
1
Most files empty in 3-unzip directory

#25 peterdfields closed 8 years ago
23
SMRT Analysis v3 download info no longer works

#24 peterdfields closed 8 years ago
2
S

#23 peterdfields closed 8 years ago
0
General refactoring

#22 pb-jchin closed 8 years ago
0
falcon_unzip and fc_unzip.cfg

#21 danshu closed 8 years ago
3

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