LAshow: Index out of bounds (Load_Read)LAshow: Index out of bounds (Load_Read)

[orangeSi]

hi,Myers. I map an bacteria draft genome to the complete genome with DAMAPPER ,when use LAshow -a to see the .las file,an error occured: LAshow: Index out of bounds (Load_Read)

thanks~

[thegenemyers]

I need a lot more information in order to be able to help you. What is the error? A crash or an error message. What was the exact sequence of command you ran, etc.

On 9/29/16, 12:12 PM, orangeSi wrote:

hi,I use map bacteria draft genome to complete genome with DAMAPPER ,when use LAshow -a ,an error happened:

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[orangeSi]

Query is bacteria draft genome,ref is the complete genome. I generate xx.las with DAMAPPER. when I ran "LAshow ref.db query.db xx.las -a ",an error( LAshow: Index out of bounds (Load_Read) )" occured.

[orangeSi]

my fault！I thought use DAMAPPER but I used daligner! now ,my command is this: step1: fasta2DAM untrimmed 991.untrimmed.reformat.fasta fasta2DAM uutig uutigs.reformat.fasta step2: DBsplit -x1000 -s200 untrimmed

step3: num=$(cat untrimmed.dam|grep blocks|awk '{print $3}') HPC.damapper -T2 -B4 -e.8 uutig untrimmed 1-$num >>run.job.sh step4： sh run.jobs.sh 2>log

step5: log file contains: LAsort: Cannot open /tmp/uutig.0〮M.las for 'r' rm: cannot remove `/tmp/uutig.0\365\025\002.M.las': No such file or directory LAsort: Cannot open /tmp/uutig.پX틪.las for 'r' rm: cannot remove /tmp/uutig.\330\376X\3737.M*.las': No such file or directory LAsort: Cannot open /tmp/uutig.پX틪.las for 'r' rm: cannot remove/tmp/uutig.\330\376X\3737.M*.las': No such file or directory 0 mapped segments 0 mapped segments 0 mapped segments

[orangeSi]

I should use "fasta2DB untrimmed 991.untrimmed.reformat.fasta" instead of "fasta2DAM untrimmed 991.untrimmed.reformat.fasta“！

[orangeSi]

Hi,Myers. I map pb subreads to genome with HPC.damapper,but still get the error when run "sh run.job.sh": 0 mapped segments LAsort: Cannot open /tmp/complete.PӮlas for 'r' sh: .M.las: command not found LAcat: No #-sign in source name 'complete.Pӧ sh: .M#.S: command not found sh: : command not found rm: cannot remove `/tmp/complete.P\325': No such file or directory sh: .M.las: command not found LAcheck: Cannot open ./part.1.complete.las for 'r'

my command is : step1: fasta2DAM complete complete.fasta fasta2DB part subread.part.fasta

step2: DBsplit -x100 -s2 part DBsplit -x100 -s2 complete num=$(cat part.db|grep blocks|awk '{print $3}') echo num is $num HPC.damapper -T2 -B4 -e.8 complete part 1-$num >>run.job.sh

step3: sh run.job.sh and get that error~

thanks~

[thegenemyers]

How big are complete and part? Could you show me the result of

cat complete.db

and

cat part.db

Then show me the result of

cat run.job.sh

Thanks, Gene

On 10/2/16, 12:32 PM, orangeSi wrote:

Hi,Myers. I map pb subreads to genome with HPC.damapper,but still get the error when run "sh run.job.sh": 0 mapped segments LAsort: Cannot open /tmp/complete.PӮlas for 'r' sh: .M/.las: command not found LAcat: No #-sign in source name 'complete.Pӧ sh: .M#.S: command not found sh: : command not found rm: cannot remove `/tmp/complete.P\325': No such file or directory sh: .M/.las: command not found LAcheck: Cannot open ./part.1.complete.las for 'r'

my command is : step1: fasta2DAM complete complete.fasta fasta2DB part subread.part.fasta

step2: DBsplit -x100 -s2 part DBsplit -x100 -s2 complete num=$(cat part.db|grep blocks|awk '{print $3}') echo num is $num HPC.damapper -T2 -B4 -e.8 complete part 1-$num >>run.job.sh

step3: sh run.job.sh and get that error~

thanks~

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[orangeSi]

complete is one bacteria genome(size 4.5M), part is 69kb which is a part of total subreads . $cat complete.dam files = 1 1 complete complete blocks = 1 size = 2000000 cutoff = 100 all = 0 0 0 1 1

$cat part.db files = 1 7 subread.part m150924_183205_42266_c100886872550000001823193303261661_s1_p0 blocks = 1 size = 2000000 cutoff = 100 all = 0 0 0 7 5

$cat run.job.sh

Damapper jobs (1)

damapper -n1 complete part.1

Check all .las files (optional but recommended)

LAcheck -vS part complete part.1.complete

[thegenemyers]

I found some bugs in the way damapper was handling /tmp files at the very end which I believe is the problem you are seeing. Could you please download the updated version of the damapper module and see if I've fixed the problem? Thanks, Gene

On 10/2/16, 4:17 PM, orangeSi wrote:

complete is one bacteria genome(size 4.5M), part is 69kb which is a part of total subreads . $cat complete.dam files = 1 1 complete complete blocks = 1 size = 2000000 cutoff = 100 all = 0 0 0 1 1

$cat part.db files = 1 7 subread.part m150924_183205_42266_c100886872550000001823193303261661_s1_p0 blocks = 1 size = 2000000 cutoff = 100 all = 0 0 0 7 5

$cat run.job.sh

Damapper jobs (1)

damapper -n1 complete part.1

Check all .las files (optional but recommended)

LAcheck -vS part complete part.1.complete

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[orangeSi]

updated version of the damapper module has fixed the problem~

thanks!