Use of freed value in iteration

zjlahey commented 2 years ago

Hi,

I receive the following error when trying to run NOVOPlasty v.4.3.1:

Reading Input......OK

Building Hash Table...Use of freed value in iteration at NOVOPlasty4.3.1.pl line 4847.

Here's the config file:

Project:

Project name = SRR2069943 Type = mito Genome Range = 12000-22000 K-mer = 33 Max memory = Extended log = 0 Save assembled reads = no Seed Input = /project/usvl_vector/NOVOPlasty/seeds/KX714952.1_Eretmocerus_sp.fasta Extend seed directly = no Reference sequence = Variance detection = Chloroplast sequence =

Dataset 1:

Read Length = 151 Insert size = 300 Platform = illumina Single/Paired = PE Combined reads = Forward reads = /project/usvl_vector/SRR2069943_pass_1.fastq Reverse reads = /project/usvl_vector/SRR2069943_pass_2.fastq Store Hash =

Heteroplasmy:

MAF = HP exclude list = PCR-free =

Optional:

Insert size auto = yes Use Quality Scores = no Output path =

Any idea what's going on?

Thanks!

ndierckx commented 2 years ago

Hi,

I never saw it before, if I google it seems it is a bug in Perl.

Is that error persistent or was it a one time thing?

jcoelho25 commented 2 years ago

Hello! I am having the exact same issue. Have you figured out how to solve this?

ndierckx commented 2 years ago

Hi,

Which OS are you using (windows, Mac or linux)?

zjlahey commented 2 years ago

Hi,

Sorry for the delayed reply. I'm using Linux. Maybe the issue has something to do with the data set that I'm using? I'm using UCE reads from the SRA (https://www.ncbi.nlm.nih.gov/sra/SRX4950810[accn]). I haven't tried running it again with a different data set.

ferrojm commented 2 years ago

Hi @zjlahey! I had a similar issue with UCE data. I renamed the reads with seqtk and it seems it solved my problem.

seqtk rename reads_1.fastq any_name > reads_modif_1.fastq seqtk rename reads_2.fastq any_name > reads_modif_2.fastq

maybe this can help you!

ndierckx commented 2 years ago

Hi,

What is UCE data? En what did you change in the read names, maybe I can make it compatible

ferrojm commented 2 years ago

Hi @ndierckx, The UCE data are Ultraconserved Element reads.

The original reads were like this:

@ERX5303696.1.1 1 length=126
TGTCTTTAGTCTTAATTCAATAGGGTACCAGGACTTGCAGACAACAAGAGGAGACCATGAACTACTGATACAGAATAAGGAGCAGTGGAAATGGCCACGAGCGCCATGGAAGTAGAAAGGCTACTT
+ERX5303696.1.1 1 length=126
BBBBBFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFBFFFFFFFFF/FBFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF/ 
@ERX5303696.2.1 2 length=126
CCCCTATTTGTTCTTTTTAATTTGGACATTAAAATATTCATATTTGAAATATGTGTGAGATTTCCTTTGAAGAGACACACTAACTTAGTTTGTTAATCAGTGGTTGCTGGCACACAGCAATTTGGG
+ERX5303696.2.1 2 length=126
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB

And after modifying their names with seqtk using the code name "Eligmo":

@Eligmo1 1 length=126
TGTCTTTAGTCTTAATTCAATAGGGTACCAGGACTTGCAGACAACAAGAGGAGACCATGAACTACTGATACAGAATAAGGAGCAGTGGAAATGGCCACGAGCGCCATGGAAGTAGAAAGGCTACTT
+
BBBBBFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFBFFFFFFFFF/FBFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF/
@Eligmo2 2 length=126
CCCCTATTTGTTCTTTTTAATTTGGACATTAAAATATTCATATTTGAAATATGTGTGAGATTTCCTTTGAAGAGACACACTAACTTAGTTTGTTAATCAGTGGTTGCTGGCACACAGCAATTTGGG
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB

ndierckx commented 2 years ago

Hi Thanks for the info, how do the reverse reads look like?

ferrojm commented 2 years ago

I renamed them using the same code name. I realized that both forward and reverse were named the same, although NOVOPlasty worked fine!

Original reverse reads:

@ERX5303696.1.2 1 length=126
AAGGTACTCACTGCCCTTCTAAGAAATCTCCTTAGACCTTGATAATACTACAAAACAGCAAAGTGATTTTAATATCTGCTTATAGAGAACAAGGTTTCATTGTGTCATTTTTAAACAAAATTTGTT
+ERX5303696.1.2 1 length=126
BBBBBFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFBFFFF
@ERX5303696.2.2 2 length=126
TGTGTACTAAGTAATGCACAGTTCTAGACAAAAAATAAAAATAAGACAGTTAAAAGAAGACAAACCACCATTATTTGTTTCCCTACCACAGGATATGCTTTCTTGTATGCCCAGTAAAATTTGAAT
+ERX5303696.2.2 2 length=126

Modified reverse reads:

@Eligmo1 1 length=126
AAGGTACTCACTGCCCTTCTAAGAAATCTCCTTAGACCTTGATAATACTACAAAACAGCAAAGTGATTTTAATATCTGCTTATAGAGAACAAGGTTTCATTGTGTCATTTTTAAACAAAATTTGTT
+
BBBBBFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFBFFFF
@Eligmo2 2 length=126
TGTGTACTAAGTAATGCACAGTTCTAGACAAAAAATAAAAATAAGACAGTTAAAAGAAGACAAACCACCATTATTTGTTTCCCTACCACAGGATATGCTTTCTTGTATGCCCAGTAAAATTTGAAT
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

ndierckx commented 2 years ago

Ok thanks, will upload a new version soon. Will let you know, maybe conversion won't be necessary anymore

ndierckx / NOVOPlasty