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correctOxford p0001 p0001.blast6.r > p0001.blast6.r.fa 2> p0001.blast6.r.log #18

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Subhi opened this issue May 9, 2017 · 0 comments
Open

correctOxford p0001 p0001.blast6.r > p0001.blast6.r.fa 2> p0001.blast6.r.log #18

Subhi opened this issue May 9, 2017 · 0 comments

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@Subhi
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Subhi commented May 9, 2017

Hi,

I am trying to use nanocorr for correction. Howver I get the following error:

Running task 1 of job nanocorr, 7390889 on mc210.fda.gov

Building a new DB, current time: 05/09/2017 12:12:21
New DB name: /tmp/7390889.1.long/p0001
New DB title: p0001
Sequence typKeep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 100 sequences in 0.00780916 seconds.
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedye: Nucleotide
_repeat_filter: Filtered Alignments 2
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 6
Remove Self: Filtered alignments: 6
greedy_repeat_filter: Staring Alignments: 6
greedy_repeat_filter: Filtered Alignments 6
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 4
Remove Self: Filtered alignments: 4
greedy_repeat_filter: Staring Alignments: 4
greedy_repeat_filter: Filtered Alignments 3
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 4
Remove Self: Filtered alignments: 4
greedy_repeat_filter: Staring Alignments: 4
greedy_repeat_filter: Filtered Alignments 3
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 3
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 3
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 4
Remove Self: Filtered alignments: 4
greedy_repeat_filter: Staring Alignments: 4
greedy_repeat_filter: Filtered Alignments 3
Remove Self: Working on 4
Remove Self: Filtered alignments: 4
greedy_repeat_filter: Staring Alignments: 4
greedy_repeat_filter: Filtered Alignments 3
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 4
Remove Self: Filtered alignments: 4
greedy_repeat_filter: Staring Alignments: 4
greedy_repeat_filter: Filtered Alignments 3
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 5
Remove Self: Filtered alignments: 5
greedy_repeat_filter: Staring Alignments: 5
greedy_repeat_filter: Filtered Alignments 5
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 3
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 4
Remove Self: Filtered alignments: 4
greedy_repeat_filter: Staring Alignments: 4
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 6
Remove Self: Filtered alignments: 6
greedy_repeat_filter: Staring Alignments: 6
greedy_repeat_filter: Filtered Alignments 3
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 4
Remove Self: Filtered alignments: 4
greedy_repeat_filter: Staring Alignments: 4
greedy_repeat_filter: Filtered Alignments 4
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 4
Remove Self: Filtered alignments: 4
greedy_repeat_filter: Staring Alignments: 4
greedy_repeat_filter: Filtered Alignments 3
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 3
Remove Self: Working on 4
Remove Self: Filtered alignments: 4
greedy_repeat_filter: Staring Alignments: 4
greedy_repeat_filter: Filtered Alignments 3
Remove Self: Working on 1
Remove Self: Filtered alignments: 1
greedy_repeat_filter: Staring Alignments: 1
greedy_repeat_filter: Filtered Alignments 1
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 3
Remove Self: Filtered alignments: 3
greedy_repeat_filter: Staring Alignments: 3
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
Remove Self: Working on 2
Remove Self: Filtered alignments: 2
greedy_repeat_filter: Staring Alignments: 2
greedy_repeat_filter: Filtered Alignments 2
sh: line 1: 25905 Aborted (core dumped) correctOxford p0001 p0001.blast6.r > p0001.blast6.r.fa 2> p0001.blast6.r.log
Running : cp /projects01/arifakhanlabs/nanocorr/runs/0001/p0001 .
Running : makeblastdb -dbtype nucl -in p0001
Running : blastn -db p0001 -query /projects01/arifakhanlabs/nanopore_files/FeLV.fasta -outfmt "6 std qlen slen qseq sseq" -dust no -task blastn -reward 5 -penalty -4 -gapopen 8 -gapextend 6 -evalue 1e-15 | sort -k 2,2 -k 9,9n > p0001.blast6
Running : cp p0001.blast6 /projects01/arifakhanlabs/nanocorr/runs/0001
Running : blast6Filter r_experimental p0001.blast6 > p0001.blast6.r
Running : cp p0001.blast6.r /projects01/arifakhanlabs/nanocorr/runs/0001
Running : correctOxford p0001 p0001.blast6.r > p0001.blast6.r.fa 2> p0001.blast6.r.log
Failed : correctOxford p0001 p0001.blast6.r > p0001.blast6.r.fa 2> p0001.blast6.r.log

real 0m2.415s
user 0m1.540s
sys 0m0.207s

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@Subhi