[mira_talk] Re: problem with miraSearchESTSNPs
- From: Bastian Greshake <bgreshake@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 17 Jun 2010 11:32:15 +0200
Hi,
Am 14.06.2010 um 21:49 schrieb Bastien Chevreux:
> Send me both logs.
attached the logs of step3 on 32 bit and 64 bit.
Cheers,
Bastian
// Bastian Greshake
// Bernhard-Ernst-Str. 21
// 48155 Münster
// cell: +49 176 213 044 66
// http://www.ruleofthirds.de
// PGP-Key-ID: 0xE6884670
This is miraEST V3.1.16 (development version) for EST SNP analysis in strains.
Please cite: Chevreux, B., Pfisterer, T., Drescher, B., Driesel, A. J.,
Mueller, W. E., Wetter, T. and Suhai, S. (2004),
Using the miraEST Assembler for Reliable and Automated mRNA Transcript
Assembly and SNP Detection in Sequenced ESTs. Genome Research, 14(6).
Mail general questions to the MIRA talk mailing list:
mira_talk@xxxxxxxxxxxxx
To (un-)subsubcribe the MIRA mailing lists, see:
http://www.chevreux.org/mira_mailinglists.html
To report bugs or ask for features, please use the new ticketing system at:
http://sourceforge.net/apps/trac/mira-assembler/
This ensures that requests don't get lost.
Compiled by: bach
Sun Jun 13 13:47:40 CEST 2010
On: Linux varcadia32 2.6.27-11-generic #1 SMP Thu Jan 29 19:24:39 UTC 2009 i686
GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compilation settings (sorry, for debug):
Size of size_t : 4
Size of uint32 : 4
Size of uint32_t: 4
Size of uint64 : 8
Size of uint64_t: 8
Current system: Linux ubuntu 2.6.32-22-generic #36-Ubuntu SMP Thu Jun 3
22:02:19 UTC 2010 i686 GNU/Linux
Parsing parameters: --job=denovo,normal,esps3 --noclipping=sanger
SANGER_SETTINGS -LR:wqf=no -AS:epoq=no
-SB:sbuip is 3, but must be no more than 1. Setting to 1
Using quickmode switch -noclipping :
SANGER_SETTINGS
-CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:lcc=no:emlc=no:emrc=no:cpat=no
COMMON_SETTINGS -CL:ascdc=no:asjdc=no
Parameters parsed without error, perfect.
Starting step 3:
clustering contigs
finding possible allelic variances
finding possible allelic variances with SNP
Creating directory step3_assembly ... done.
Creating directory step3_assembly/step3_d_log ... done.
Creating directory step3_assembly/step3_d_results ... done.
Creating directory step3_assembly/step3_d_info ... done.
Creating directory step3_assembly/step3_d_chkpt ... done.
Localtime: Thu Jun 17 01:24:57 2010
Loading project from CAF file: step2_reads.caf
First counting reads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Now simulating loading of data:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Sanger will load 68 reads.
Longest Sanger: 1881
Longest 454: 0
Longest PacBio: 0
Longest Solexa: 0
Longest Solid: 0
Longest overall: 1881
Total reads to load: 68
Reserving space for reads
Reserved space for 78 reads.
Loading project from CAF file: step2_reads.caf
Now loading and processing data:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Loaded 68 Sanger reads.
Total reads loaded: 68
========================== Memory self assessment ==============================
Running in 32 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 1026472 kB
MemFree: 540052 kB
Buffers: 34104 kB
Cached: 188096 kB
SwapCached: 19320 kB
Active: 198420 kB
Inactive: 255000 kB
Active(anon): 109268 kB
Inactive(anon): 126648 kB
Active(file): 89152 kB
Inactive(file): 128352 kB
Unevictable: 20 kB
Mlocked: 20 kB
HighTotal: 139208 kB
HighFree: 252 kB
LowTotal: 887264 kB
LowFree: 539800 kB
SwapTotal: 916472 kB
SwapFree: 811660 kB
Dirty: 22192 kB
Writeback: 0 kB
AnonPages: 216832 kB
Mapped: 45396 kB
Shmem: 4696 kB
Slab: 17352 kB
SReclaimable: 8596 kB
SUnreclaim: 8756 kB
KernelStack: 2184 kB
PageTables: 5836 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 1429708 kB
Committed_AS: 1061724 kB
VmallocTotal: 122880 kB
VmallocUsed: 6508 kB
VmallocChunk: 111488 kB
HardwareCorrupted: 0 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 4096 kB
DirectMap4k: 16376 kB
DirectMap4M: 892928 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: miraSearchESTSN
State: R (running)
Tgid: 9921
Pid: 9921
PPid: 9919
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 32
Groups: 4 20 24 46 105 119 122 1000
VmPeak: 7220 kB
VmSize: 7220 kB
VmLck: 0 kB
VmHWM: 2732 kB
VmRSS: 2732 kB
VmData: 2948 kB
VmStk: 84 kB
VmExe: 4164 kB
VmLib: 0 kB
VmPTE: 24 kB
Threads: 1
SigQ: 0/16382
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000006
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: 1
Cpus_allowed_list: 0
Mems_allowed: 1
Mems_allowed_list: 0
voluntary_ctxt_switches: 6
nonvoluntary_ctxt_switches: 49
Stack usage: 12 kB
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 68 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 759260 (741 KiB)
Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 0 12 B 0 B 0 B
AS_skim_edges: 0 12 B 0 B 0 B
AS_adsfacts: 0 12 B 0 B 0 B
AS_confirmed_edges: 0 12 B 0 B 0 B
AS_permanent_overlap_bans: 0 12 B 0 B 0 B
AS_readhitmiss: 0 12 B 0 B 0 B
AS_readhmcovered: 0 12 B 0 B 0 B
AS_count_rhm: 0 12 B 0 B 0 B
AS_clipleft: 0 12 B 0 B 0 B
AS_clipright: 0 12 B 0 B 0 B
AS_used_ids: 0 12 B 0 B 0 B
AS_multicopies: 0 12 B 0 B 0 B
AS_hasmcoverlaps: 0 12 B 0 B 0 B
AS_maxcoveragereached: 0 12 B 0 B 0 B
AS_coverageperseqtype: 0 12 B 0 B 0 B
AS_istroublemaker: 0 12 B 0 B 0 B
AS_isdebris: 0 12 B 0 B 0 B
AS_needalloverlaps: 0 20 B 0 B 0 B
AS_readsforrepeatresolve: 0 20 B 0 B 0 B
AS_allrmbsok: 0 12 B 0 B 0 B
AS_probablermbsnotok: 0 12 B 0 B 0 B
AS_weakrmbsnotok: 0 12 B 0 B 0 B
AS_readmaytakeskim: 0 20 B 0 B 0 B
AS_skimstaken: 0 20 B 0 B 0 B
AS_numskimoverlaps: 0 12 B 0 B 0 B
AS_numleftextendskims: 0 12 B 0 B 0 B
AS_rightextendskims: 0 12 B 0 B 0 B
AS_skimleftextendratio: 0 12 B 0 B 0 B
AS_skimrightextendratio: 0 12 B 0 B 0 B
AS_usedlogfiles: 0 8 B 0 B 0 B
Total: 759648 (742 KiB)
================================================================================
Localtime: Thu Jun 17 01:24:57 2010
Checking SCF files (loading qualities only if needed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
0 SCF files loaded ok.
68 SCF files were not found (see
'step3_assembly/step3_d_log/step3_info_scfreadfail.0' for a list of names).
Localtime: Thu Jun 17 01:24:57 2010
Loading straindata.
Building hash table ... done. Assigning strains to reads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Read 68 straindata lines.
Checking reads for trace data:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
No SCF data present in any read, automatic contig editing for Sanger data is
now switched off.
68 reads with valid data for assembly.
Localtime: Thu Jun 17 01:24:57 2010
Generated 68 unique template ids for 68 valid reads.
No useful template information found, template routines will not be used.
Localtime: Thu Jun 17 01:24:57 2010
Seeing strain 1: "remain"
Generated 1 unique strain ids for 68 reads.
Strain "default" has 0 reads.
Strain "remain" has 68 reads.
Have read pool with 68 reads.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 PacBio Solexa SOLiD
----------------------------------------
Total reads 68 0 0 0 0
Reads wo qual 0 0 0 0 0
Used reads 68 0 0 0 0
Avg tot rlen 1085 0 0 0 0
Avg rlen used 1085 0 0 0 0
With strain 68 0 0 0 0
W/o clips 0 0 0 0 0
===========================================================================
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 PacBio Solexa SOLiD
----------------------------------------
Total reads 68 0 0 0 0
Reads wo qual 0 0 0 0 0
Used reads 68 0 0 0 0
Avg tot rlen 1085 0 0 0 0
Avg rlen used 1085 0 0 0 0
With strain 68 0 0 0 0
W/o clips 0 0 0 0 0
===========================================================================
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Hash statistics:
=========================================================
Measured avg. frequency coverage: 2
Deduced thresholds:
-------------------
Min normal cov: 1
Max normal cov: 3
Repeat cov: 4
Heavy cov: 16
Crazy cov: 40
Mask cov: 200
Repeat ratio histogram:
-----------------------
1 1334
2 122
3 14
4 10
7 2
=========================================================
Assigning statistics values:
Localtime: Thu Jun 17 01:24:58 2010
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Thu Jun 17 01:24:59 2010
Searching for possible overlaps:
Localtime: Thu Jun 17 01:24:59 2010
Now running threaded and partitioned skimmer with 1 partitions in 2 threads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done.
Skim summary:
accepted: 0
possible: 2
permbans: 0
Hits chosen: 0
Localtime: Thu Jun 17 01:24:59 2010
Total megahubs: 0
System memory: 1051107328
Mem2keepfree: 157666099
Used by MIRA: 170455040
Mem avail: 722986189
rsh not increased.
DBG: TSH 0
Max seen block 1: 0
Max num skim edges: 89478485
Can load up to 0 skim edges at once.
Partitioning into 0 blocks.
Max seen block 2: 0
We have 0 skims in file.
Has short reads: 0
Localtime: Thu Jun 17 01:24:59 2010
De-normalising SKIM hits ... (this will take a while)
Localtime: Thu Jun 17 01:24:59 2010
Localtime: Thu Jun 17 01:24:59 2010
Only against rails: 0
Step 0
Localtime: Thu Jun 17 01:24:59 2010
Only long reads
Step 10
Total skims taken: 0
Step 20
Total skims taken: 0
Step 30
Total skims taken: 0
Step 40
Total skims taken: 0
Step 50
Total skims taken: 0
Step 55
Total skims taken: 0
Step 60
Total skims taken: 0
Step NAO
rsh4_takeNeedAllOverlaps.
Taken 0 hits.
Total skims taken: 0
Filtering forward skims.
Localtime: Thu Jun 17 01:24:59 2010
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Done.
Filtering complement skims.
Localtime: Thu Jun 17 01:24:59 2010
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Done all filtering.
Nuking AS_skimrightextendratio
Nuking AS_skimleftextendratio
Nuking AS_numrightextendskims
Nuking AS_numleftextendskims
Nuking AS_numskimoverlaps
Nuking AS_readmaytakeskim
Nuking AS_skimstaken
Nuking AS_skim_edges
Pre-assembly alignment search for read extension and / or vector clipping:
Making alignments.
Localtime: Thu Jun 17 01:24:59 2010
Aligning possible forward matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Alignment stats:
Potential: 0
Calculated: 0
Evaded (PB): 0
Rejected (checkfun): 0
Trans 100 saved: 0
Banned overlap pairs: 0 in 0 reads.
Localtime: Thu Jun 17 01:24:59 2010
Aligning possible complement matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Alignment stats:
Potential: 0
Calculated: 0
Evaded (PB): 0
Rejected (checkfun): 0
Trans 100 saved: 0
Banned overlap pairs: 0 in 0 reads.
Localtime: Thu Jun 17 01:24:59 2010
Localtime: Thu Jun 17 01:24:59 2010
Counting number of alignments in file ... done.
Expecting 0 alignments.
Localtime: Thu Jun 17 01:24:59 2010
Loading confirmed overlaps from disk (will need approximately 0 B RAM):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Thu Jun 17 01:24:59 2010
Sorting confirmed overlaps (this may take a while) ... done.
Localtime: Thu Jun 17 01:24:59 2010
Generating clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Sorting clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Writing clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Writing unclustered reads ... done.
Pre-assembly read extension:
Localtime: Thu Jun 17 01:24:59 2010
Searching possible read extensions (for Sanger and/or 454):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Changed length of 0 sequences.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 PacBio Solexa SOLiD
----------------------------------------
Total reads 68 0 0 0 0
Reads wo qual 0 0 0 0 0
Used reads 68 0 0 0 0
Avg tot rlen 1085 0 0 0 0
Avg rlen used 1085 0 0 0 0
With strain 68 0 0 0 0
W/o clips 0 0 0 0 0
===========================================================================
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Hash statistics:
=========================================================
Measured avg. frequency coverage: 2
Deduced thresholds:
-------------------
Min normal cov: 1
Max normal cov: 3
Repeat cov: 4
Heavy cov: 16
Crazy cov: 40
Mask cov: 200
Repeat ratio histogram:
-----------------------
1 1334
2 122
3 14
4 10
7 2
=========================================================
Assigning statistics values:
Localtime: Thu Jun 17 01:25:00 2010
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Thu Jun 17 01:25:01 2010
Searching for possible overlaps:
Localtime: Thu Jun 17 01:25:01 2010
Now running threaded and partitioned skimmer with 1 partitions in 2 threads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done.
Skim summary:
accepted: 0
possible: 2
permbans: 0
Hits chosen: 0
Localtime: Thu Jun 17 01:25:02 2010
Total megahubs: 0
System memory: 1051107328
Mem2keepfree: 157666099
Used by MIRA: 178458624
Mem avail: 714982605
rsh not increased.
DBG: TSH 0
Max seen block 1: 0
Max num skim edges: 89478485
Can load up to 0 skim edges at once.
Partitioning into 0 blocks.
Max seen block 2: 0
We have 0 skims in file.
Has short reads: 0
Localtime: Thu Jun 17 01:25:02 2010
De-normalising SKIM hits ... (this will take a while)
Localtime: Thu Jun 17 01:25:02 2010
Localtime: Thu Jun 17 01:25:02 2010
Only against rails: 0
Step 0
Localtime: Thu Jun 17 01:25:02 2010
Only long reads
Step 10
Total skims taken: 0
Step 20
Total skims taken: 0
Step 30
Total skims taken: 0
Step 40
Total skims taken: 0
Step 50
Total skims taken: 0
Step 55
Total skims taken: 0
Step 60
Total skims taken: 0
Step NAO
rsh4_takeNeedAllOverlaps.
Taken 0 hits.
Total skims taken: 0
Filtering forward skims.
Localtime: Thu Jun 17 01:25:02 2010
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Done.
Filtering complement skims.
Localtime: Thu Jun 17 01:25:02 2010
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Done all filtering.
Nuking AS_skimrightextendratio
Nuking AS_skimleftextendratio
Nuking AS_numrightextendskims
Nuking AS_numleftextendskims
Nuking AS_numskimoverlaps
Nuking AS_readmaytakeskim
Nuking AS_skimstaken
Nuking AS_skim_edges
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: miraSearchESTSN
State: R (running)
Tgid: 9921
Pid: 9921
PPid: 9919
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 32
Groups: 4 20 24 46 105 119 122 1000
VmPeak: 174280 kB
VmSize: 174276 kB
VmLck: 0 kB
VmHWM: 139300 kB
VmRSS: 139300 kB
VmData: 170004 kB
VmStk: 84 kB
VmExe: 4164 kB
VmLib: 0 kB
VmPTE: 164 kB
Threads: 2
SigQ: 0/16382
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000006
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: 1
Cpus_allowed_list: 0
Mems_allowed: 1
Mems_allowed_list: 0
voluntary_ctxt_switches: 55
nonvoluntary_ctxt_switches: 817
Stack usage: 20 kB
--------------------------------------------------------------------------------
Pass: 1
Making alignments.
Localtime: Thu Jun 17 01:25:02 2010
Aligning possible forward matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Alignment stats:
Potential: 0
Calculated: 0
Evaded (PB): 0
Rejected (checkfun): 0
Trans 100 saved: 0
Banned overlap pairs: 0 in 0 reads.
Localtime: Thu Jun 17 01:25:02 2010
Aligning possible complement matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Alignment stats:
Potential: 0
Calculated: 0
Evaded (PB): 0
Rejected (checkfun): 0
Trans 100 saved: 0
Banned overlap pairs: 0 in 0 reads.
Localtime: Thu Jun 17 01:25:02 2010
Localtime: Thu Jun 17 01:25:02 2010
Counting number of alignments in file ... done.
Expecting 0 alignments.
Localtime: Thu Jun 17 01:25:02 2010
Loading confirmed overlaps from disk (will need approximately 0 B RAM):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Thu Jun 17 01:25:02 2010
Sorting confirmed overlaps (this may take a while) ... done.
Localtime: Thu Jun 17 01:25:02 2010
Generating clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Sorting clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Writing clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Writing unclustered reads ... done.
BFC: 1 1
overlapcompressstepping: 68
nextoverlapcompress: 68
Moving small clusters to debris:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done. 0 reads moved to debris.
bfc 1
Localtime: Thu Jun 17 01:25:02 2010
bfc 2
Saving debris list to file:
step3_assembly/step3_d_info/step3_info_debrislist.txt
Saving debris list to file:
step3_assembly/step3_d_info/step3_info_debrislist.txt
Localtime: Thu Jun 17 01:25:02 2010
Localtime: Thu Jun 17 01:25:02 2010
Localtime: Thu Jun 17 01:25:02 2010
Localtime: Thu Jun 17 01:25:02 2010
Localtime: Thu Jun 17 01:25:02 2010
Localtime: Thu Jun 17 01:25:02 2010
Localtime: Thu Jun 17 01:25:02 2010
Localtime: Thu Jun 17 01:25:02 2010
Localtime: Thu Jun 17 01:25:02 2010
Saving SNP list to file: step3_assembly/step3_d_info/step3_info_snplist.txt
========================== Memory self assessment ==============================
Running in 32 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 1026472 kB
MemFree: 401420 kB
Buffers: 34724 kB
Cached: 188568 kB
SwapCached: 19308 kB
Active: 335716 kB
Inactive: 255924 kB
Active(anon): 246452 kB
Inactive(anon): 126648 kB
Active(file): 89264 kB
Inactive(file): 129276 kB
Unevictable: 20 kB
Mlocked: 20 kB
HighTotal: 139208 kB
HighFree: 252 kB
LowTotal: 887264 kB
LowFree: 401168 kB
SwapTotal: 916472 kB
SwapFree: 811672 kB
Dirty: 22384 kB
Writeback: 208 kB
AnonPages: 353964 kB
Mapped: 46148 kB
Shmem: 4700 kB
Slab: 17384 kB
SReclaimable: 8624 kB
SUnreclaim: 8760 kB
KernelStack: 2192 kB
PageTables: 5988 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 1429708 kB
Committed_AS: 1230136 kB
VmallocTotal: 122880 kB
VmallocUsed: 6508 kB
VmallocChunk: 111488 kB
HardwareCorrupted: 0 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 4096 kB
DirectMap4k: 16376 kB
DirectMap4M: 892928 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: miraSearchESTSN
State: R (running)
Tgid: 9921
Pid: 9921
PPid: 9919
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 32
Groups: 4 20 24 46 105 119 122 1000
VmPeak: 174280 kB
VmSize: 174276 kB
VmLck: 0 kB
VmHWM: 139424 kB
VmRSS: 139424 kB
VmData: 170004 kB
VmStk: 84 kB
VmExe: 4164 kB
VmLib: 0 kB
VmPTE: 164 kB
Threads: 1
SigQ: 0/16382
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000006
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: 1
Cpus_allowed_list: 0
Mems_allowed: 1
Mems_allowed_list: 0
voluntary_ctxt_switches: 55
nonvoluntary_ctxt_switches: 822
Stack usage: 20 kB
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 68 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 759288 (741 KiB)
Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 68 284 B 0 B 0 B
AS_skim_edges: 0 12 B 0 B 0 B
AS_adsfacts: 0 12 B 0 B 0 B
AS_confirmed_edges: 0 12 B 0 B 0 B
AS_permanent_overlap_bans: 0 2 KiB 0 B 0 B
AS_readhitmiss: 0 12 B 0 B 0 B
AS_readhmcovered: 0 12 B 0 B 0 B
AS_count_rhm: 0 12 B 0 B 0 B
AS_clipleft: 68 284 B 0 B 0 B
AS_clipright: 68 284 B 0 B 0 B
AS_used_ids: 0 80 B 68 B 0 B
AS_multicopies: 68 80 B 0 B 0 B
AS_hasmcoverlaps: 0 80 B 68 B 0 B
AS_maxcoveragereached: 68 284 B 0 B 0 B
AS_coverageperseqtype: 0 12 B 0 B 0 B
AS_istroublemaker: 68 80 B 0 B 0 B
AS_isdebris: 68 80 B 0 B 0 B
AS_needalloverlaps: 68 116 B 28 B 0 B
AS_readsforrepeatresolve: 0 20 B 0 B 0 B
AS_allrmbsok: 0 12 B 0 B 0 B
AS_probablermbsnotok: 0 12 B 0 B 0 B
AS_weakrmbsnotok: 0 12 B 0 B 0 B
AS_readmaytakeskim: 0 20 B 0 B 0 B
AS_skimstaken: 0 20 B 0 B 0 B
AS_numskimoverlaps: 0 12 B 0 B 0 B
AS_numleftextendskims: 0 12 B 0 B 0 B
AS_rightextendskims: 0 12 B 0 B 0 B
AS_skimleftextendratio: 0 12 B 0 B 0 B
AS_skimrightextendratio: 0 12 B 0 B 0 B
AS_usedlogfiles: 30 488 B 0 B 0 B
Total: 763312 (745 KiB)
================================================================================
Dynamic allocs: 0
Align allocs: 0
End of assembly process, thank you for using miraEST.
This is miraEST V3.0.0 (production version) for EST SNP analysis in strains.
Please cite: Chevreux, B., Pfisterer, T., Drescher, B., Driesel, A. J.,
Mueller, W. E., Wetter, T. and Suhai, S. (2004),
Using the miraEST Assembler for Reliable and Automated mRNA Transcript
Assembly and SNP Detection in Sequenced ESTs. Genome Research, 14(6).
Mail general questions to the MIRA talk mailing list:
mira_talk@xxxxxxxxxxxxx
To (un-)subsubcribe the MIRA mailing lists, see:
http://www.chevreux.org/mira_mailinglists.html
To report bugs or ask for features, please use the new ticketing system at:
http://sourceforge.net/apps/trac/mira-assembler/
This ensures that requests don't get lost.
Compiled by: root
Tue Feb 9 11:57:18 CET 2010
On: Linux EBBSRV08 2.6.26-2-amd64 #1 SMP Wed Aug 19 22:33:18 UTC 2009 x86_64
GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compilation settings (sorry, for debug):
Size of size_t : 8
Size of uint32 : 4
Size of uint32_t: 4
Size of uint64 : 8
Size of uint64_t: 8
Current system: Linux EBBSRV08 2.6.26-2-amd64 #1 SMP Wed Aug 19 22:33:18 UTC
2009 x86_64 GNU/Linux
Parsing parameters: --job=normal,denovo,esps3 --noclipping=sanger
-SB:sbuip is 3, but must be no more than 1. Setting to 1
Using quickmode switch -noclipping :
SANGER_SETTINGS
-CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:lcc=no:emlc=no:emrc=no:cpat=no
Parameters parsed without error, perfect.
Starting step 3:
clustering contigs
finding possible allelic variances
finding possible allelic variances with SNP
Creating directory step3_assembly ... done.
Creating directory step3_assembly/step3_d_log ... done.
Creating directory step3_assembly/step3_d_results ... done.
Creating directory step3_assembly/step3_d_info ... done.
Creating directory step3_assembly/step3_d_chkpt ... done.
Localtime: Thu Jun 17 11:04:49 2010
Loading project from CAF file: step2_reads.caf
First counting reads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Now simulating loading of data:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Sanger will load 68 reads.
Longest Sanger: 1877
Longest 454: 0
Longest Solexa: 0
Longest Solid: 0
Longest overall: 1877
Total reads to load: 68
Reserving space for reads
Reserved space for 78 reads.
Loading project from CAF file: step2_reads.caf
Now loading and processing data:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Loaded 68 Sanger reads.
Total reads loaded: 68
Localtime: Thu Jun 17 11:04:49 2010
Checking SCF files (loading qualities only if needed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
0 SCF files loaded ok.
68 SCF files were not found (see
'step3_assembly/step3_d_log/step3_info_scfreadfail.0' for a list of names).
Localtime: Thu Jun 17 11:04:49 2010
Loading straindata.
Building hash table ... done. Assigning strains to reads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Read 68 straindata lines.
Checking reads for trace data:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
No SCF data present in any read, automatic contig editing for Sanger data is
now switched off.
68 reads with valid data for assembly.
Localtime: Thu Jun 17 11:04:49 2010
Generated 68 unique template ids for 68 valid reads.
No useful template information found, template routines will not be used.
Localtime: Thu Jun 17 11:04:49 2010
Seeing strain 1: "remain"
Generated 1 unique strain ids for 68 reads.
Strain "default" has 0 reads.
Strain "remain" has 68 reads.
Have read pool with 68 reads.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 Solexa SOLiD
---------------------------------
Total reads 68 0 0 0
Reads wo qual 0 0 0 0
Used reads 68 0 0 0
Avg len used 1042 0 0 0
With strain 68 0 0 0
W/o clips 0 0 0 0
===========================================================================
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 Solexa SOLiD
---------------------------------
Total reads 68 0 0 0
Reads wo qual 0 0 0 0
Used reads 68 0 0 0
Avg len used 1042 0 0 0
With strain 68 0 0 0
W/o clips 0 0 0 0
===========================================================================
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Hash statistics:
=========================================================
Measured avg. frequency coverage: 2
Deduced thresholds:
-------------------
Min normal cov: 0.8
Max normal cov: 3.2
Repeat cov: 3.8
Heavy cov: 16
Crazy cov: 40
Mask cov: 200
Repeat ratio histogram:
-----------------------
1 1424
2 356
3 20
4 44
5 10
19 2
=========================================================
Assigning statistics values:
Localtime: Thu Jun 17 11:04:50 2010
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Correcting by RMB:
Localtime: Thu Jun 17 11:04:50 2010
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Thu Jun 17 11:04:50 2010
Searching for possible overlaps:
Localtime: Thu Jun 17 11:04:50 2010
Now running threaded and partitioned skimmer with 1 partitions in 2 threads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done.
Skim summary:
accepted: 1
possible: 15
permbans: 0
Hits chosen: 1
Localtime: Thu Jun 17 11:04:50 2010
Total megahubs: 0
System memory: 66643841024
Mem2keepfree: 6664384102
Used by MIRA: 118652928
Mem avail: 59860803994
rsh increased memtouse to: 59860803994
Can load up to 2 skim edges at once.
We have 1 skims in file.
Localtime: Thu Jun 17 11:04:50 2010
De-normalising SKIM hits ... (this will take a while)
Only one block ... first loop ...not loaded yet.
Loading skims in id range 0 to 68
Loaded 2 elements.
Sorting ... done.
Only one block ... not in first loop, return 0.
Localtime: Thu Jun 17 11:04:50 2010
Loading block 0
Only one block, already loaded.
Localtime: Thu Jun 17 11:04:50 2010
Step 0
Loading block 0
Only one block, already loaded.
Localtime: Thu Jun 17 11:04:50 2010
Only long reads
Step 10
Loading block 0
Only one block, already loaded.
Step 20
Loading block 0
Only one block, already loaded.
Step 30
Loading block 0
Only one block, already loaded.
Step 40
Loading block 0
Only one block, already loaded.
Step 50
Loading block 0
Only one block, already loaded.
Step 60
Loading block 0
Only one block, already loaded.
Step NAO
rsh4_takeNeedAllOverlaps.
Loading block 0
Only one block, already loaded.
Taken 0 hits.
Total skims taken: 1
Filtering forward skims.
Localtime: Thu Jun 17 11:04:50 2010
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Done.
Filtering complement skims.
Localtime: Thu Jun 17 11:04:50 2010
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Done.
Pass: 1
Making alignments.
Localtime: Thu Jun 17 11:04:50 2010
Aligning possible forward matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Alignment stats:
Potential: 0
Calculated: 0
Evaded (PB): 0
Rejected (checkfun): 0
Trans 100 saved: 0
Banned overlap pairs: 0 in 0 reads.
Localtime: Thu Jun 17 11:04:50 2010
Aligning possible complement matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Alignment stats:
Potential: 1
Calculated: 1
Evaded (PB): 0
Rejected (checkfun): 0
Trans 100 saved: 0
Banned overlap pairs: 0 in 0 reads.
Localtime: Thu Jun 17 11:04:50 2010
Localtime: Thu Jun 17 11:04:50 2010
Counting number of alignments in file ... done.
Expecting 1 alignments.
Localtime: Thu Jun 17 11:04:50 2010
Loading confirmed overlaps from disk (will need approximately 60 B RAM):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Thu Jun 17 11:04:50 2010
Sorting confirmed overlaps (this may take a while) ... done.
Localtime: Thu Jun 17 11:04:50 2010
Generating clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Sorting clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Writing clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Writing unclustered reads ... done.
overlapcompressstepping: 68
nextoverlapcompress: 68
Localtime: Thu Jun 17 11:04:50 2010
Building new contig 1
Localtime: Thu Jun 17 11:04:50 2010
Unused reads: 2
+[1] +
Finished building.
Localtime: Thu Jun 17 11:04:50 2010
-------------- Contig statistics ----------------
Contig id: 1
Contig length: 1101
Sanger 454 Solexa SOLiD
Num. reads 2 0 0 0
100% merged reads - - 0 0
Avg. read len 792 0 0 0
Max. coverage 2 0 0 0
Avg. coverage 1.440 0.000 0.000 0.000
Max. contig coverage: 2
Avg. contig coverage: 1.440
Consensus contains: A: 222 C: 273 G: 291 T: 285 N: 1
IUPAC: 29 Funny: 0 *: 0
GC content: 52.661%
-------------------------------------------------
Localtime: Thu Jun 17 11:04:50 2010
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Transfering reads to readpool.
Done.
Storing contig ... Searching for SNPs and IUPACs, preparing needed data:
sorting tags ... fetching consensus for strain0 ...(strain 0 empty.)
...fetching consensus for strain1 ...done.
Starting search:
done with search
Transfering tags to readpool.
done.
Localtime: Thu Jun 17 11:04:51 2010
Saving debris list to file:
step3_assembly/step3_d_info/step3_info_debrislist.txt
Saving debris list to file:
step3_assembly/step3_d_info/step3_info_debrislist.txt
Localtime: Thu Jun 17 11:04:51 2010
Localtime: Thu Jun 17 11:04:51 2010
Localtime: Thu Jun 17 11:04:51 2010
Localtime: Thu Jun 17 11:04:51 2010
Localtime: Thu Jun 17 11:04:51 2010
Localtime: Thu Jun 17 11:04:51 2010
Localtime: Thu Jun 17 11:04:51 2010
Localtime: Thu Jun 17 11:04:51 2010
Localtime: Thu Jun 17 11:04:51 2010
Saving SNP list to file: step3_assembly/step3_d_info/step3_info_snplist.txt
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 65081876 kB
MemFree: 46816596 kB
Buffers: 300828 kB
Cached: 17172160 kB
SwapCached: 0 kB
Active: 3051372 kB
Inactive: 14475660 kB
SwapTotal: 31248376 kB
SwapFree: 31248376 kB
Dirty: 4 kB
Writeback: 0 kB
AnonPages: 53504 kB
Mapped: 16840 kB
Slab: 582916 kB
SReclaimable: 570188 kB
SUnreclaim: 12728 kB
PageTables: 3468 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 63789312 kB
Committed_AS: 252312 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 402424 kB
VmallocChunk: 34359335643 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: miraSearchESTSN
State: R (running)
Tgid: 13507
Pid: 13507
PPid: 13348
TracerPid: 0
Uid: 199129 199129 199129 199129
Gid: 1704 1704 1704 1704
FDSize: 256
Groups: 1704
VmPeak: 443948 kB
VmSize: 115880 kB
VmLck: 0 kB
VmHWM: 266168 kB
VmRSS: 7068 kB
VmData: 91036 kB
VmStk: 92 kB
VmExe: 2764 kB
VmLib: 3436 kB
VmPTE: 108 kB
Threads: 1
SigQ: 0/522239
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: 000000ff
Cpus_allowed_list: 0-7
Mems_allowed: 00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 835
nonvoluntary_ctxt_switches: 1
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 68 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 730728 (714 KiB)
Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 68 296 B 0 B 0 B
AS_skim_edges: 0 24 B 0 B 0 B
AS_adsfacts: 1 48 B 0 B 4 B
AS_confirmed_edges: 2 64 B 0 B 0 B
AS_permanent_overlap_bans: 0 3 KiB 0 B 0 B
AS_readhitmiss: 0 24 B 0 B 0 B
AS_readhmcovered: 0 24 B 0 B 0 B
AS_count_rhm: 0 24 B 0 B 0 B
AS_clipleft: 68 296 B 0 B 0 B
AS_clipright: 68 296 B 0 B 0 B
AS_used_ids: 0 96 B 68 B 4 B
AS_multicopies: 68 96 B 0 B 4 B
AS_hasmcoverlaps: 0 96 B 68 B 4 B
AS_maxcoveragereached: 68 296 B 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 68 96 B 0 B 4 B
AS_isdebris: 68 96 B 0 B 4 B
AS_needalloverlaps: 68 168 B 60 B 0 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 24 B 0 B 0 B
AS_probablermbsnotok: 0 24 B 0 B 0 B
AS_weakrmbsnotok: 0 24 B 0 B 0 B
AS_readmaytakeskim: 0 40 B 0 B 0 B
AS_skimstaken: 0 40 B 0 B 0 B
AS_numskimoverlaps: 0 24 B 0 B 0 B
AS_numleftextendskims: 0 24 B 0 B 0 B
AS_rightextendskims: 0 24 B 0 B 0 B
AS_skimleftextendratio: 0 24 B 0 B 0 B
AS_skimrightextendratio: 0 24 B 0 B 0 B
AS_usedlogfiles: 29 944 B 0 B 0 B
Total: 737336 (720 KiB)
================================================================================
Dynamic allocs: 4
Align allocs: 4
End of assembly process, thank you for using miraEST.
Other related posts:
