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Generade-nl / TULIP

TULIP - The Uncorrected Long read Itegration Pipeline
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Tulip bulb: Use of uninitialized value in concatenation #4

Closed gringer closed 7 years ago

gringer commented 7 years ago

I thought this error was due to TULIP's expectation that the FASTA input file(s) will be one line per read (as per the FASTQ convention) rather than being wrapped at some number of characters (as per the FASTA convention). This does seem to be the case in at least the readFasta method:

       for (my $i = 1; $i < $fbuffer; $i++) {                                                                                               
                my $headerin = <FASTA>;                                                                                                      
                my $seqin = <FASTA>;

However, even after altering my input files to a single line per sequence, I'm still getting this error (albeit less frequently):

$ perl ~/install/tulip/tulipbulb.perl --seeds unique_unitig_fragments_800bp_50gap.fasta --sam 132394_vs_unique_unitigs.shortsam --input tulip/NBL5_ONTA --reads 132394.fasta --out bulb/NBL5_ONTA
Run started
Seed length is 800
Retrieving graph from tulip/NBL5_ONTA.graph_tmp
Retrieving scaffolds from tulip/NBL5_ONTA.scaffolds_tmp
Retrieving scaffold seeds from tulip/NBL5_ONTA.seeds_tmp
28364 seeds in the graph
Bundling sam coordinates from 132394_vs_unique_unitigs.shortsam with reads from 132394.fasta
Use of uninitialized value in concatenation (.) or string at /home/gringer/install/tulip/tulipbulb.perl line 544, <FASTA> line 12825.
Use of uninitialized value in concatenation (.) or string at /home/gringer/install/tulip/tulipbulb.perl line 544, <FASTA> line 187023.
10000 lines read
20000 lines read
30000 lines read
40000 lines read
Use of uninitialized value in concatenation (.) or string at /home/gringer/install/tulip/tulipbulb.perl line 544, <FASTA> line 841193.
Use of uninitialized value $sequence in substr at /home/gringer/install/tulip/tulipbulb.perl line 569, <FASTA> line 841193.
substr outside of string at /home/gringer/install/tulip/tulipbulb.perl line 569, <FASTA> line 841193.
Use of uninitialized value $seq in string eq at /home/gringer/install/tulip/tulipbulb.perl line 689, <FASTA> line 841193.
Use of uninitialized value $seq in transliteration (tr///) at /home/gringer/install/tulip/tulipbulb.perl line 690, <FASTA> line 841193.
Use of uninitialized value $seq in reverse at /home/gringer/install/tulip/tulipbulb.perl line 691, <FASTA> line 841193.
Use of uninitialized value in concatenation (.) or string at /home/gringer/install/tulip/tulipbulb.perl line 544, <FASTA> line 894001.
Use of uninitialized value $sequence in substr at /home/gringer/install/tulip/tulipbulb.perl line 569, <FASTA> line 894001.
substr outside of string at /home/gringer/install/tulip/tulipbulb.perl line 569, <FASTA> line 894001.
Use of uninitialized value $seq in string eq at /home/gringer/install/tulip/tulipbulb.perl line 689, <FASTA> line 894001.
Use of uninitialized value $seq in transliteration (tr///) at /home/gringer/install/tulip/tulipbulb.perl line 690, <FASTA> line 894001.
Use of uninitialized value $seq in reverse at /home/gringer/install/tulip/tulipbulb.perl line 691, <FASTA> line 894001.
50000 lines read
60000 lines read
Generade-nl commented 7 years ago

This appears a duplicate issue of Generade-nl/TULIP#1

This is probably caused by the reshuffling of read and seed index numbers in the alignment file compared to the original data files. Due to multi-thread alignment; reads and seeds could end up in a different order in the alignment file.

We will continue solving the problem using issue Generade-nl/TULIP#1, for now this issue is closed

Any problems, please send us an e-mail. Thank you.