I am trying to design oligoprobes using OligoMiner tool in windows subsystem linux (wsl) by activating anaconda software. Please have a loo to th ecommands given below. in the middle i am facing an error of Index error and I am not able to fix it. I copied the fasta DNA files into Oligominer folder before giving commands in wsl. these were as follows: (ol) rahul@DESKTOP-J3Q9JD9:~/ol_dir/OligoMiner$ python blockParse.py 5.fa
0 of 345789
100000 of 345789
200000 of 345789
6635 candidate probes identified in 345.77 kb yielding 19.19 candidates/kb
Program took 14.599275 seconds
(ol) rahul@DESKTOP-J3Q9JD9:~/ol_dir/OligoMiner$ bowtie2-build 5.fa 5
Settings:
Output files: "5.*.bt2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
5.fa
Building a SMALL index
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 86447
Using parameters --bmax 64836 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 64836 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:00
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:00
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:00
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 345789 (target: 64835)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 1
No samples; assembling all-inclusive block
Sorting block of length 345789 for bucket 1
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 345790 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 82484
fchr[G]: 168573
fchr[T]: 263073
fchr[$]: 345789
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4309819 bytes to primary EBWT file: 5.1.bt2
Wrote 86452 bytes to secondary EBWT file: 5.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 345789
bwtLen: 345790
sz: 86448
bwtSz: 86448
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 21612
offsSz: 86448
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 1801
numLines: 1801
ebwtTotLen: 115264
ebwtTotSz: 115264
color: 0
reverse: 0
Total time for call to driver() for forward index: 00:00:00
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 86447
Using parameters --bmax 64836 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 64836 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:00
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:00
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:00
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 345789 (target: 64835)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 1
No samples; assembling all-inclusive block
Sorting block of length 345789 for bucket 1
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 345790 for bucket 1
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 82484
fchr[G]: 168573
fchr[T]: 263073
fchr[$]: 345789
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4309819 bytes to primary EBWT file: 5.rev.1.bt2
Wrote 86452 bytes to secondary EBWT file: 5.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 345789
bwtLen: 345790
sz: 86448
bwtSz: 86448
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 21612
offsSz: 86448
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 1801
numLines: 1801
ebwtTotLen: 115264
ebwtTotSz: 115264
color: 0
reverse: 1
Total time for backward call to driver() for mirror index: 00:00:01
(ol) rahul@DESKTOP-J3Q9JD9:~/ol_dir/OligoMiner$ bowtie2 -x ~/ol_dir/OligoMiner$ bowtie2 -x ~/ol_dir/OligoMiner/5 -U 5.fa
stq --no-hd -t -k 100 --very-sensitive-local -S 5_u.sam
(ERR): "/home/rahul/ol_dir/OligoMiner$" does not exist or is not a Bowtie 2 index
Exiting now ...
(ol) rahul@DESKTOP-J3Q9JD9:~/ol_dir/OligoMiner$ bowtie2 -x ~/ol_dir/OligoMiner/5 -U 5.fa
Error: reads file does not look like a FASTQ file
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134
(ol) rahul@DESKTOP-J3Q9JD9:~/ol_dir/OligoMiner$ bowtie2 -x ~/ol_dir/OligoMiner/5 -U 5.fastq --no-hd -t -k 100 --very-sensitive-local -S 5_u.sam
Time loading reference: 00:00:00
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
Multiseed full-index search: 00:00:00
6635 reads; of these:
6635 (100.00%) were unpaired; of these:
0 (0.00%) aligned 0 times
6578 (99.14%) aligned exactly 1 time
57 (0.86%) aligned >1 times
100.00% overall alignment rate
Time searching: 00:00:00
Overall time: 00:00:00
(ol) rahul@DESKTOP-J3Q9JD9:~/ol_dir/OligoMiner$ python outputClean.py -u -f 5_u.sam
Traceback (most recent call last):
File "outputClean.py", line 486, in <module>
main()
File "outputClean.py", line 480, in main
reportVal, debugVal, metaVal, outNameVal, startTime)
File "outputClean.py", line 70, in cleanOutput
if x[0] is not '@' else ' ' for x in file_read]
IndexError: list index out of range
(ol) rahul@DESKTOP-J3Q9JD9:~/ol_dir/OligoMiner$
I was trying Anaconda activated environment where Oligominer tool was used to create oligoprobes from the input DNA fasta file. I was expecting to get the probes after the commands given but could not get them.
