Index error in wsl while running oligominer in Anaconda

Question

[Rahul]

Hey all, 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. Please have a look to the last command which gave error. Command from the start 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$

Answer 1

[Polina]

You have a typo in a code: bowtie2 -x ~/ol_dir/OligoMiner$ bowtie2 -x ~/ol_dir/OligoMiner/5 -U 5.fa

Should be: bowtie2 -x ~/ol_dir/OligoMiner/5 -U 5.fa