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NOVOPlasty - The organelle assembler and heteroplasmy caller
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Weird statistics in the log file #118

Open DenisGoryunov opened 4 years ago

DenisGoryunov commented 4 years ago

Hello Nicolas, I tried to assemble PE reads from Sequence Read Archive (SRA). In the log file i got:

Subsampled fraction: 97.43 % Forward reads without pair: 2707262 Reverse reads without pair: 517327

When i performed wc -l unix command on the files with forward and reverse reads i obtained the same numbers:

wc -l R1.fastq 172878812 wc -l R2.fastq 172878812

How that may be possible? What is wrong with my fastq files?

Best, Denis

ndierckx commented 4 years ago

Hi,

Whats the SRA number?

DenisGoryunov commented 4 years ago

SRR6856357

ndierckx commented 4 years ago

And the assembly didn't work? If not can you send me the end of your forward and reverse files, just use tail to show the last 20 lines or so

DenisGoryunov commented 4 years ago

I got just one 20 kb contig instead of the complete genome and was thinking that's because of the incorrect format of my fastq files. May that be a reason of the incomplete assembly? Do you need file examples in that case?

ndierckx commented 4 years ago

Yeah send the ends of the file, must be a problem with the read ids... When submitted to SRA they often don't have their original id structure

DenisGoryunov commented 4 years ago

Nicolas, Please find the file examples in attachment.

Regards, Denis

ср, 11 дек. 2019 г. в 19:24, Nicolas Dierckxsens notifications@github.com:

Yeah send the ends of the file, must be a problem with the read ids... When submitted to SRA they often don't have their original id structure

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@SRR6856357.49127110 49127110 length=151 TCACAATCTTCACACTTACTCATTCTCATAGAGAGGTTTTTCTTGAAAAGTTCTTTCTCTTTCTCTCTATCATTTCCTTCTTGATTTAAAAAAGAAAAACACGAGATGTCGAGTAAGAAGAGGAGTTCGAAGAAAG +SRR6856357.49127110 49127110 length=151 JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJJJJJJJJJJJJJJJJJJJ-A<AAAJFFJAJFFJFJJFJAF7AJJFJJJJJJ @SRR6856357.49127111 49127111 length=151 CTTCAAGTACTCTATGTCGCGATCCACGTCGAGCTCTTCAACATACTTCACCATTTCATCGGAGAAAGCTTCCTTTGCCTCGTTCAGTTCTGCCCACCAAACTCTACGAACAGTGAACTGCACAAAGACCAAGACA +SRR6856357.49127111 49127111 length=151 JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFAJJJFJFJJJJJJJJJJJJJJJJJJJJ @SRR6856357.49127113 49127113 length=151 ATCTTAAAAAAATACTAAAATTTATTAACACTGATAATCGTGCACGTAGGTCGTGAAGGAGCATGTAAAGTTTACCAACCGTTGCAAAGTCGACACTAAAGTCTAAACCAAAACAAAATGCGACTTTAGAAATGTT +SRR6856357.49127113 49127113 length=151 JJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<JJJJFJJJJJJJJJJJJFJJJJJJJJJJJFJJJJJJJFJJJFJJJFJJJJJJJJJJJJJJJAFJJJJFFJJJJJJJJJJJJJJJJJJJJAJJJJFJJJJJFAA @SRR6856357.49127114 49127114 length=151 TATTCAGGAGTTAACATTGTTGTAAGTTATCATATCTTAACTCTAACATGTAAATTTGAGACACTTTCTGAGACATCATAATCCTATGTATTTATCAAACTTGTCCCCAAAAGAAGCTCGTAAGACACTTGAAAGT +SRR6856357.49127114 49127114 length=151 JJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJ @SRR6856357.49127115 49127115 length=151 CGGAACAACAGGACAAGAAGCGGCCAAGACATCCTAAGCCTTGCCAAGCTAGTCTAACCACCTAAGCCCTAAGTTCTCTAAGCTAGCAGGAGTTCTCTAATTCTAAATTCTCGGATCCCCTTTTCTTCTGCTCCTT +SRR6856357.49127115 49127115 length=151 JJJJAJJFJFJJJJJJJJJJJJJJJJJJJ<FFAJAJJFJJJJJFJJJJJJJAJFJJJJJJJJJJJJJJJFJFJJ<AJJJFJJJJJJJ-JJ-<AF-<JJA-AAFJJJJJFJJJJJ<JFJJFJJFJFAFJFFF7FJJF

@SRR6856357.49127110 49127110 length=151 CAAGGACCCTTTCTTCGAACTCCTCTTCTTACTCGACATCTCGTGTTTTTCTTTTTTAANTCAAGAAGGAAATGATAGAGAGAAAGAGAAAGAACTTTTCAAGAAAAACCTCTCTATGAGAATGAGTAAGTGTGAA +SRR6856357.49127110 49127110 length=151 JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ#JFJJJJFFJJJJJJFJJFAFAJFF<FJJJ7AJFJJJJJJJFJFAFJJFJJAJJJJF7F<F7<FA-A-7AFAF<FFA @SRR6856357.49127111 49127111 length=151 TGACTCCCCTAGACACCGAAGAATGCTTCAACAACAATGTAAGTTTCTCTCTCTTCTTTNATGTTCTAATCTTCATCTTTGTCTGTTTTGGTAAGTAACAAAATGTCTTGGTCTTTGTGCAGTTCACTGTTCGTAG +SRR6856357.49127111 49127111 length=151 JJJJJJFJJJAA<FFJJJF7AJJJJJJJJJJJJJJJJJJJJAFAJFJJJJJJJJJJJJJ#JJJJJJJJJJJJJJJJJJJJJJJJJFFFFFJJJFAJF<JA<7FJJJJJJJJJJAAJJJJJFJJJJJ<FFFJJJF-A @SRR6856357.49127113 49127113 length=151 AGCTGCTTGACAGAGACGGCATTGCCAATTTGCCACTTGCTTTCTTTTGTCCTGATTAANCAAGAGCGTATCGTTAATAATATTTGTACAAAGCACAACTTAGTTAGGCCTCTACCAGTAAACACTCGCCTAGAAC +SRR6856357.49127113 49127113 length=151 FJJJJJJJJJJJJJJJJJJJJJJF7FJFJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJ#FJJJAJJJFJAJJAF<-FFFFJJJJJJJJJ-AJJJJJJFFFJJJ<FJJJFJJJJ<FFJJ<F-7AFJJJJFJF--A7 @SRR6856357.49127114 49127114 length=151 TTCTCTCTTCTATTACAACAAGTCTCTTATGCCTCTCCCAATATCTATGTACTTTCAAGNGTCTTACGAGCTTCTTTTGGGGACAAGTTTGATAAATACATAGGATTATGATGTCTCAGAAAGTGTCTCAAATTT +SRR6856357.49127114 49127114 length=151 JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJAAA#FFJJJFJF7FJFAFJJFFJJJJJJ<AFJJJJJJJJFJAA7A-<A77<JAFJJFAJJJJJ<F7FJJF<AFF--A<F @SRR6856357.49127115 49127115 length=151 TGAAGGCGAAGGATGGGCCACCGACCTAGAGCGACTATATAAGGAGAGAAGGAGCAGAANAAAAGGGGATCCGAGAATTTAGAATTAGAGAACTCCTGCTAGCTTAGAGAACTTAGGGCTTAGGTGGTTAGACTAG +SRR6856357.49127115 49127115 length=151 J<JJJJJJF7JJFFJJJJAFJJFJJJJFJFJJJJJFFJJJJJJJJJ-FJJJJJJJJJJJ#FFJFFF<JFFJJJFJ-FJFAFJJFJJFJJJJAFJFAFJJJJJJJJFJJJF7FFA<FJJ<<)A<F77A<JJJFJ<FF

ndierckx commented 4 years ago

sorry could you send the first 5 too? They look different than on the ncbi SRA viewer

DenisGoryunov commented 4 years ago

Nicolas,

Please find the files you asked me for in attachment.

Regards, Denis

ср, 11 дек. 2019 г. в 22:38, Nicolas Dierckxsens notifications@github.com:

sorry could you send the first 5 too? They look different than on the ncbi SRA viewer

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@SRR6856357.2 2 length=151 TCCTCACACTGTCGGTACTCATTATTCATTAATATGGTAAAATCTAAAGGTTTCAAATTACAAATCCACTCTTCTTACGAAAAAATAACCTAATTTATATTTCTTAATTAAACGTGATCAAA +SRR6856357.2 2 length=151 FJJJFJJJJFJFJJ7-FJJJJF-<JJJJJFAFAJAJJ7JFJFFFFFJJJF7AA<-FAJ-F<<FF7AJF7JF-AJAAJFJ7A7J-<<JJJA-AA-77AA--7FFFFJAFFJFA77<7<-7F-< @SRR6856357.4 4 length=151

@SRR6856357.2 2 length=151 TGCAGGTACATAAACCATTTATGTTTCATATGATAAGGACGAACATTTCATGCATGCAAATAGCTAGACCTATTACTTATCTTCCATATATTTGATCACGT +SRR6856357.2 2 length=151 JFJJJFAJAJJJJJJJA-FJJ<<FFJJJJJF-J--AAJ7F7A7A<-77AF7FAF-7AFAF-7AAAAFFJF7AJFAJFF7<-7<--A7<<-7<-AJ77-AFA @SRR6856357.4 4 length=151

ndierckx commented 4 years ago

NOVOPlasty3.7.3_TEST.zip

Can you run it with this version, you can cancel after a few seconds, it will output something with "TEST" behind, just send me that line

DenisGoryunov commented 4 years ago

Hi, You mean this information from the log file: " Reading Input...

identical TEST

...OK

Scan reference sequence......OK

Building Hash Table......OK

Subsampled fraction: 97.43 % Forward reads without pair: 2707262 Reverse reads without pair: 517327

Retrieve Seed......OK "

ср, 11 дек. 2019 г. в 23:39, Nicolas Dierckxsens notifications@github.com:

NOVOPlasty3.7.3_TEST.zip https://github.com/ndierckx/NOVOPlasty/files/3952472/NOVOPlasty3.7.3_TEST.zip

Can you run it with this version, you can cancel after a few seconds, it will output something with "TEST" behind, just send me that line

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ndierckx commented 4 years ago

Ok thanks and sorry but could you send me the log file completely, just to see what you filled in the config file...

DenisGoryunov commented 4 years ago

Please find the log file in the attachment.

Regards, Denis

чт, 12 дек. 2019 г. в 16:53, Nicolas Dierckxsens notifications@github.com:

Ok thanks and sorry but could you send me the log file completely, just to see what you filled in the config file...

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NOVOPlasty: The Organelle Assembler Version 3.7.3 Author: Nicolas Dierckxsens, (c) 2015-2019

Batch file detected...

Input parameters from the configuration file: Verify if everything is correct

Project:

Project name = Project1 Type = chloro Genome range = 12000-22000 K-mer = 39 Max memory = Extended log = 0 Save assembled reads = no Seed Input = NC_016734-rbcL_gene.fasta Reference sequence = NC_016734_R.fasta Variance detection = Chloroplast sequence =

Dataset 1:

Read Length = 136 Insert size = Platform = illumina Single/Paired = PE Combined reads = Forward reads = SRR6856357_1_t.fastq.gz Reverse reads = SRR6856357_2_t.fastq.gz

Heteroplasmy:

Heteroplasmy = HP exclude list = PCR-free =

Optional:

Insert size auto = yes Insert range = 1.8 Insert range strict = 1.3 Use Quality Scores =

Reading Input...

identical TEST

...OK

Scan reference sequence......OK

Building Hash Table......OK

Subsampled fraction: 97.43 % Forward reads without pair: 2707262 Reverse reads without pair: 517327

Retrieve Seed......OK

Initial read retrieved successfully: TTCCTAATTTATGTCGAGTAGACCTTGTTGTTTTGTTTTATTGCAAGAATTCTAAATTCATGACTTGTAGGGAGGGACTTATGTCACCACAAACAGAGACTAAAGCAAGTGTTGGATTCAAAGCTGGTGTTAAAG

Start Assembly...

135 bp assembled 135 bp assembled 174 bp assembled 203 bp assembled 284 bp assembled 325 bp assembled 367 bp assembled 398 bp assembled 440 bp assembled 449 bp assembled 495 bp assembled 512 bp assembled 548 bp assembled 620 bp assembled 652 bp assembled 684 bp assembled 734 bp assembled 759 bp assembled 773 bp assembled 828 bp assembled 902 bp assembled 931 bp assembled 991 bp assembled 1046 bp assembled 1114 bp assembled 1176 bp assembled 1233 bp assembled 1285 bp assembled 1363 bp assembled 1384 bp assembled 1409 bp assembled 1442 bp assembled 1553 bp assembled 1580 bp assembled 1613 bp assembled 1653 bp assembled 1750 bp assembled 1776 bp assembled 1794 bp assembled 1823 bp assembled 1941 bp assembled 1978 bp assembled 2034 bp assembled 2068 bp assembled 2170 bp assembled 2194 bp assembled 2210 bp assembled 2266 bp assembled 2354 bp assembled 2432 bp assembled 2460 bp assembled 2478 bp assembled 2549 bp assembled 2618 bp assembled 2653 bp assembled 2687 bp assembled 2814 bp assembled 2839 bp assembled 2883 bp assembled 2931 bp assembled 3030 bp assembled 3036 bp assembled 3062 bp assembled 3129 bp assembled 3201 bp assembled 3219 bp assembled 3275 bp assembled 3313 bp assembled 3431 bp assembled 3481 bp assembled 3511 bp assembled 3554 bp assembled 3611 bp assembled 3633 bp assembled 3683 bp assembled 3684 bp assembled 3691 bp assembled 3712 bp assembled 3715 bp assembled 3733 bp assembled 3777 bp assembled 3777 bp assembled 3777 bp assembled 3779 bp assembled 3837 bp assembled 3887 bp assembled 3887 bp assembled 3887 bp assembled 3887 bp assembled 3914 bp assembled 3914 bp assembled 3914 bp assembled 3914 bp assembled 3955 bp assembled 3955 bp assembled 3955 bp assembled 3955 bp assembled 4001 bp assembled 4001 bp assembled 4001 bp assembled 4001 bp assembled 4058 bp assembled 4058 bp assembled 4058 bp assembled 4058 bp assembled 4083 bp assembled 4083 bp assembled 4083 bp assembled 4083 bp assembled 4160 bp assembled 4160 bp assembled 4160 bp assembled 4160 bp assembled 4213 bp assembled 4213 bp assembled 4213 bp assembled 4213 bp assembled 4246 bp assembled 4306 bp assembled 4333 bp assembled 4333 bp assembled 4333 bp assembled 4333 bp assembled 4375 bp assembled 4439 bp assembled 4464 bp assembled 4495 bp assembled 4495 bp assembled 4495 bp assembled 4495 bp assembled 4541 bp assembled 4541 bp assembled 4541 bp assembled 4541 bp assembled 4579 bp assembled 4614 bp assembled 4614 bp assembled 4614 bp assembled 4614 bp assembled 4655 bp assembled 4714 bp assembled 4714 bp assembled 4714 bp assembled 4714 bp assembled 4739 bp assembled 4739 bp assembled 4739 bp assembled 4739 bp assembled 4788 bp assembled 4788 bp assembled 4788 bp assembled 4788 bp assembled 4849 bp assembled 4883 bp assembled 4883 bp assembled 4883 bp assembled 4883 bp assembled 4918 bp assembled 4918 bp assembled 4918 bp assembled 4918 bp assembled 4978 bp assembled 4978 bp assembled 4978 bp assembled 4978 bp assembled 5001 bp assembled 5001 bp assembled 5001 bp assembled 5001 bp assembled 5046 bp assembled 5046 bp assembled 5046 bp assembled 5046 bp assembled 5112 bp assembled 5112 bp assembled 5112 bp assembled 5112 bp assembled 5152 bp assembled 5200 bp assembled 5200 bp assembled 5200 bp assembled 5200 bp assembled 5226 bp assembled 5285 bp assembled 5339 bp assembled 5339 bp assembled 5339 bp assembled 5339 bp assembled 5380 bp assembled 5380 bp assembled 5380 bp assembled 5380 bp assembled 5414 bp assembled 5414 bp assembled 5414 bp assembled 5414 bp assembled 5458 bp assembled 5458 bp assembled 5458 bp assembled 5458 bp assembled 5503 bp assembled 5503 bp assembled 5503 bp assembled 5503 bp assembled 5546 bp assembled 5546 bp assembled 5546 bp assembled 5546 bp assembled 5602 bp assembled 5602 bp assembled 5602 bp assembled 5602 bp assembled 5631 bp assembled 5631 bp assembled 5631 bp assembled 5631 bp assembled 5659 bp assembled 5659 bp assembled 5659 bp assembled 5659 bp assembled 5671 bp assembled 5671 bp assembled 5671 bp assembled 5671 bp assembled 5717 bp assembled 5717 bp assembled 5717 bp assembled 5717 bp assembled 5791 bp assembled 5791 bp assembled 5791 bp assembled 5791 bp assembled 5821 bp assembled 5821 bp assembled 5821 bp assembled 5821 bp assembled 5852 bp assembled 5852 bp assembled 5852 bp assembled 5852 bp assembled 5900 bp assembled 5900 bp assembled 5900 bp assembled 5900 bp assembled 5950 bp assembled 5950 bp assembled 5950 bp assembled 5950 bp assembled 5997 bp assembled 5997 bp assembled 5997 bp assembled 5997 bp assembled 6045 bp assembled 6071 bp assembled 6071 bp assembled 6071 bp assembled 6071 bp assembled 6116 bp assembled 6116 bp assembled 6116 bp assembled 6116 bp assembled 6157 bp assembled 6157 bp assembled 6157 bp assembled 6157 bp assembled 6188 bp assembled 6188 bp assembled 6188 bp assembled 6188 bp assembled 6226 bp assembled 6226 bp assembled 6226 bp assembled 6226 bp assembled 6281 bp assembled 6281 bp assembled 6281 bp assembled 6281 bp assembled 6319 bp assembled 6319 bp assembled 6319 bp assembled 6319 bp assembled 6362 bp assembled 6427 bp assembled 6427 bp assembled 6427 bp assembled 6427 bp assembled 6454 bp assembled 6454 bp assembled 6454 bp assembled 6454 bp assembled 6498 bp assembled 6498 bp assembled 6498 bp assembled 6498 bp assembled 6520 bp assembled 6539 bp assembled 6539 bp assembled 6539 bp assembled 6539 bp assembled 6596 bp assembled 6596 bp assembled 6596 bp assembled 6596 bp assembled 6657 bp assembled 6657 bp assembled 6657 bp assembled 6657 bp assembled 6701 bp assembled 6727 bp assembled 6727 bp assembled 6727 bp assembled 6727 bp assembled 6758 bp assembled 6835 bp assembled 6852 bp assembled 6852 bp assembled 6852 bp assembled 6852 bp assembled 6871 bp assembled 6871 bp assembled 6871 bp assembled 6871 bp assembled 6921 bp assembled 6921 bp assembled 6921 bp assembled 6921 bp assembled 6966 bp assembled 6966 bp assembled 6966 bp assembled 6966 bp assembled 7021 bp assembled 7021 bp assembled 7021 bp assembled 7021 bp assembled 7067 bp assembled 7098 bp assembled 7098 bp assembled 7098 bp assembled 7098 bp assembled 7125 bp assembled 7192 bp assembled 7192 bp assembled 7192 bp assembled 7192 bp assembled 7240 bp assembled 7240 bp assembled 7240 bp assembled 7240 bp assembled 7286 bp assembled 7286 bp assembled 7286 bp assembled 7286 bp assembled 7321 bp assembled 7321 bp assembled 7321 bp assembled 7321 bp assembled 7362 bp assembled 7362 bp assembled 7362 bp assembled 7362 bp assembled 7401 bp assembled 7401 bp assembled 7401 bp assembled 7401 bp assembled 7471 bp assembled 7471 bp assembled 7471 bp assembled 7471 bp assembled 7520 bp assembled 7549 bp assembled 7549 bp assembled 7549 bp assembled 7549 bp assembled 7591 bp assembled 7591 bp assembled 7591 bp assembled 7591 bp assembled 7617 bp assembled 7617 bp assembled 7617 bp assembled 7617 bp assembled 7682 bp assembled 7682 bp assembled 7682 bp assembled 7682 bp assembled 7721 bp assembled 7721 bp assembled 7721 bp assembled 7721 bp assembled 7749 bp assembled 7749 bp assembled 7749 bp assembled 7749 bp assembled 7782 bp assembled 7782 bp assembled 7782 bp assembled 7782 bp assembled 7810 bp assembled 7810 bp assembled 7810 bp assembled 7810 bp assembled 7883 bp assembled 7883 bp assembled 7883 bp assembled 7883 bp assembled 7922 bp assembled 7922 bp assembled 7922 bp assembled 7922 bp assembled 7949 bp assembled 7949 bp assembled 7949 bp assembled 7949 bp assembled 7996 bp assembled 7996 bp assembled 7996 bp assembled 7996 bp assembled 8066 bp assembled 8066 bp assembled 8066 bp assembled 8066 bp assembled 8086 bp assembled 8086 bp assembled 8086 bp assembled 8086 bp assembled 8141 bp assembled 8141 bp assembled 8141 bp assembled 8141 bp assembled 8198 bp assembled 8224 bp assembled 8261 bp assembled 8261 bp assembled 8261 bp assembled 8261 bp assembled 8299 bp assembled 8360 bp assembled 8360 bp assembled 8360 bp assembled 8360 bp assembled 8380 bp assembled 8380 bp assembled 8380 bp assembled 8380 bp assembled 8458 bp assembled 8458 bp assembled 8458 bp assembled 8458 bp assembled 8466 bp assembled 8466 bp assembled 8466 bp assembled 8466 bp assembled 8514 bp assembled 8514 bp assembled 8514 bp assembled 8514 bp assembled 8590 bp assembled 8590 bp assembled 8590 bp assembled 8590 bp assembled 8607 bp assembled 8647 bp assembled 8647 bp assembled 8647 bp assembled 8647 bp assembled 8680 bp assembled 8680 bp assembled 8680 bp assembled 8680 bp assembled 8753 bp assembled 8753 bp assembled 8753 bp assembled 8753 bp assembled 8816 bp assembled 8816 bp assembled 8816 bp assembled 8816 bp assembled 8853 bp assembled 8853 bp assembled 8853 bp assembled 8853 bp assembled 8898 bp assembled 8898 bp assembled 8898 bp assembled 8898 bp assembled 8950 bp assembled 8950 bp assembled 8950 bp assembled 8950 bp assembled 9011 bp assembled 9011 bp assembled 9011 bp assembled 9011 bp assembled 9060 bp assembled 9120 bp assembled 9120 bp assembled 9120 bp assembled 9120 bp assembled 9135 bp assembled 9135 bp assembled 9135 bp assembled 9135 bp assembled 9196 bp assembled 9196 bp assembled 9196 bp assembled 9196 bp assembled 9217 bp assembled 9217 bp assembled 9217 bp assembled 9217 bp assembled 9286 bp assembled 9286 bp assembled 9286 bp assembled 9286 bp assembled 9312 bp assembled 9312 bp assembled 9312 bp assembled 9312 bp assembled 9378 bp assembled 9378 bp assembled 9378 bp assembled 9378 bp assembled 9402 bp assembled 9422 bp assembled 9492 bp assembled 9492 bp assembled 9492 bp assembled 9492 bp assembled 9531 bp assembled 9531 bp assembled 9531 bp assembled 9531 bp assembled 9568 bp assembled 9568 bp assembled 9568 bp assembled 9568 bp assembled 9626 bp assembled 9626 bp assembled 9626 bp assembled 9626 bp assembled 9667 bp assembled 9667 bp assembled 9667 bp assembled 9667 bp assembled 9693 bp assembled 9693 bp assembled 9693 bp assembled 9693 bp assembled 9748 bp assembled 9748 bp assembled 9748 bp assembled 9748 bp assembled 9794 bp assembled 9794 bp assembled 9794 bp assembled 9794 bp assembled 9831 bp assembled 9831 bp assembled 9831 bp assembled 9831 bp assembled 9895 bp assembled 9895 bp assembled 9895 bp assembled 9895 bp assembled 9935 bp assembled 9935 bp assembled 9935 bp assembled 9935 bp assembled 9977 bp assembled 9977 bp assembled 9977 bp assembled 9977 bp assembled 10012 bp assembled 10012 bp assembled 10012 bp assembled 10012 bp assembled 10070 bp assembled 10070 bp assembled 10070 bp assembled 10070 bp assembled 10106 bp assembled 10152 bp assembled 10152 bp assembled 10152 bp assembled 10152 bp assembled 10188 bp assembled 10188 bp assembled 10188 bp assembled 10188 bp assembled 10236 bp assembled 10236 bp assembled 10236 bp assembled 10236 bp assembled 10265 bp assembled 10265 bp assembled 10265 bp assembled 10265 bp assembled 10325 bp assembled 10325 bp assembled 10325 bp assembled 10325 bp assembled 10350 bp assembled 10350 bp assembled 10350 bp assembled 10350 bp assembled 10394 bp assembled 10394 bp assembled 10394 bp assembled 10394 bp assembled 10445 bp assembled 10445 bp assembled 10445 bp assembled 10445 bp assembled 10487 bp assembled 10487 bp assembled 10487 bp assembled 10487 bp assembled 10532 bp assembled 10551 bp assembled 10551 bp assembled 10551 bp assembled 10551 bp assembled 10574 bp assembled 10574 bp assembled 10574 bp assembled 10574 bp assembled 10628 bp assembled 10628 bp assembled 10628 bp assembled 10628 bp assembled 10694 bp assembled 10694 bp assembled 10694 bp assembled 10694 bp assembled 10711 bp assembled 10711 bp assembled 10711 bp assembled 10711 bp assembled 10774 bp assembled 10815 bp assembled 10815 bp assembled 10815 bp assembled 10815 bp assembled 10846 bp assembled 10846 bp assembled 10846 bp assembled 10846 bp assembled 10876 bp assembled 10876 bp assembled 10876 bp assembled 10876 bp assembled 10936 bp assembled 10936 bp assembled 10936 bp assembled 10936 bp assembled 10977 bp assembled 10977 bp assembled 10977 bp assembled 10977 bp assembled 11053 bp assembled 11053 bp assembled 11053 bp assembled 11053 bp assembled 11065 bp assembled 11089 bp assembled 11089 bp assembled 11089 bp assembled 11089 bp assembled 11142 bp assembled 11169 bp assembled 11169 bp assembled 11169 bp assembled 11169 bp assembled 11233 bp assembled 11233 bp assembled 11233 bp assembled 11233 bp assembled 11268 bp assembled 11298 bp assembled 11298 bp assembled 11298 bp assembled 11298 bp assembled 11339 bp assembled 11339 bp assembled 11339 bp assembled 11339 bp assembled 11393 bp assembled 11393 bp assembled 11393 bp assembled 11393 bp assembled 11420 bp assembled 11420 bp assembled 11420 bp assembled 11420 bp assembled 11476 bp assembled 11476 bp assembled 11476 bp assembled 11476 bp assembled 11512 bp assembled 11512 bp assembled 11512 bp assembled 11512 bp assembled 11576 bp assembled 11576 bp assembled 11576 bp assembled 11576 bp assembled 11603 bp assembled 11603 bp assembled 11603 bp assembled 11603 bp assembled 11653 bp assembled 11653 bp assembled 11653 bp assembled 11653 bp assembled 11706 bp assembled 11745 bp assembled 11745 bp assembled 11745 bp assembled 11745 bp assembled 11770 bp assembled 11770 bp assembled 11770 bp assembled 11770 bp assembled 11817 bp assembled 11817 bp assembled 11817 bp assembled 11817 bp assembled 11855 bp assembled 11855 bp assembled 11855 bp assembled 11855 bp assembled 11932 bp assembled 11932 bp assembled 11932 bp assembled 11932 bp assembled 11971 bp assembled 11971 bp assembled 11971 bp assembled 11971 bp assembled 12023 bp assembled 12023 bp assembled 12023 bp assembled 12023 bp assembled 12064 bp assembled 12064 bp assembled 12064 bp assembled 12064 bp assembled 12104 bp assembled 12104 bp assembled 12104 bp assembled 12104 bp assembled 12159 bp assembled 12159 bp assembled 12159 bp assembled 12159 bp assembled 12192 bp assembled 12192 bp assembled 12192 bp assembled 12192 bp assembled 12233 bp assembled 12233 bp assembled 12233 bp assembled 12233 bp assembled 12266 bp assembled 12266 bp assembled 12266 bp assembled 12266 bp assembled 12328 bp assembled 12328 bp assembled 12328 bp assembled 12328 bp assembled 12371 bp assembled 12371 bp assembled 12371 bp assembled 12371 bp assembled 12404 bp assembled 12404 bp assembled 12404 bp assembled 12404 bp assembled 12439 bp assembled 12439 bp assembled 12439 bp assembled 12439 bp assembled 12476 bp assembled 12499 bp assembled 12513 bp assembled 12513 bp assembled 12513 bp assembled 12513 bp assembled 12558 bp assembled 12620 bp assembled 12620 bp assembled 12620 bp assembled 12620 bp assembled 12661 bp assembled 12661 bp assembled 12661 bp assembled 12661 bp assembled 12688 bp assembled 12688 bp assembled 12688 bp assembled 12688 bp assembled 12739 bp assembled 12739 bp assembled 12739 bp assembled 12739 bp assembled 12783 bp assembled 12783 bp assembled 12783 bp assembled 12783 bp assembled 12825 bp assembled 12825 bp assembled 12825 bp assembled 12825 bp assembled 12850 bp assembled 12850 bp assembled 12850 bp assembled 12850 bp assembled 12927 bp assembled 12982 bp assembled 12982 bp assembled 12982 bp assembled 12982 bp assembled 13011 bp assembled 13011 bp assembled 13011 bp assembled 13011 bp assembled 13027 bp assembled 13027 bp assembled 13027 bp assembled 13027 bp assembled 13049 bp assembled 13106 bp assembled 13106 bp assembled 13106 bp assembled 13106 bp assembled 13161 bp assembled 13161 bp assembled 13161 bp assembled 13161 bp assembled 13179 bp assembled 13179 bp assembled 13179 bp assembled 13179 bp assembled 13195 bp assembled 13195 bp assembled 13195 bp assembled 13195 bp assembled 13239 bp assembled 13271 bp assembled 13326 bp assembled 13326 bp assembled 13326 bp assembled 13326 bp assembled 13360 bp assembled 13360 bp assembled 13360 bp assembled 13360 bp assembled 13410 bp assembled 13410 bp assembled 13410 bp assembled 13410 bp assembled 13456 bp assembled 13499 bp assembled 13499 bp assembled 13499 bp assembled 13499 bp assembled 13540 bp assembled 13540 bp assembled 13540 bp assembled 13540 bp assembled 13580 bp assembled 13580 bp assembled 13580 bp assembled 13580 bp assembled 13650 bp assembled 13650 bp assembled 13650 bp assembled 13650 bp assembled 13714 bp assembled 13714 bp assembled 13714 bp assembled 13714 bp assembled 13760 bp assembled 13788 bp assembled 13788 bp assembled 13788 bp assembled 13788 bp assembled 13861 bp assembled 13861 bp assembled 13861 bp assembled 13861 bp assembled 13900 bp assembled 13931 bp assembled 13931 bp assembled 13931 bp assembled 13931 bp assembled 13985 bp assembled 13985 bp assembled 13985 bp assembled 13985 bp assembled 14018 bp assembled 14018 bp assembled 14018 bp assembled 14018 bp assembled 14053 bp assembled 14101 bp assembled 14101 bp assembled 14101 bp assembled 14101 bp assembled 14138 bp assembled

ndierckx commented 4 years ago

Hi,

I downloaded the files from SRA and it works fine for me, so I don't understand the problem. How do you donwloaded the files? I added the assembly results I got:

Circularized_assembly_1_test_id.zip

DenisGoryunov commented 4 years ago

Hello Nicolas, Many thanks for your help! Did you remove the adapters before the assembly? Would you recommend to do it usually prior the assembly?

The fastq files were sent to me by my colleague. As i know he processed them in trimmomatic (well known software, typically can not destroy correct reads order in paired fastq files). I verified the order of paired-end reads in that fastq files by bbmap:

Input is being processed as paired Input: 86439406 reads 11255907057 bases Output: 86439406 reads (100.00%) 11255907057 bases (100.00%)

Time: 116.980 seconds. Reads Processed: 86439k 738.92k reads/sec Bases Processed: 11255m 96.22m bases/sec Names appear to be correctly paired.

So, obviously everything is fine with the order of read names in the both fastq files, but it seems Novoplasty can not treat them correctly for some reason. But anyway i fully agree with you that it's much better to use the raw reads for assembly.

Regards, Denis

вт, 17 дек. 2019 г. в 01:52, Nicolas Dierckxsens notifications@github.com:

Hi,

I downloaded the files from SRA and it works fine for me, so I don't understand the problem. How do you donwloaded the files? I added the assembly results I got:

Circularized_assembly_1_test_id.zip https://github.com/ndierckx/NOVOPlasty/files/3970525/Circularized_assembly_1_test_id.zip

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DenisGoryunov commented 4 years ago

I wonder did you found the weird statistics regarding reads number without pair in initial fastq files like i sent you before?

ndierckx commented 4 years ago

Hi, No I didn't had that, everything worked fine. And I downloaded the original files, so something must happend afterwards. I never trim for adapters, but maybe in some cases it could be useful, I am not sure. I added the latest version that is not online yet, I ran it with that one, maybe it will go...

NOVOPlasty3.7.3.zip

DenisGoryunov commented 4 years ago

Hello Nicolas,

Thank you again.

Regards, Denis

чт, 19 дек. 2019 г. в 13:30, Nicolas Dierckxsens notifications@github.com:

Hi, No I didn't had that, everything worked fine. And I downloaded the original files, so something must happend afterwards. I never trim for adapters, but maybe in some cases it could be useful, I am not sure. I added the latest version that is not online yet, I ran it with that one, maybe it will go...

NOVOPlasty3.7.3.zip https://github.com/ndierckx/NOVOPlasty/files/3983020/NOVOPlasty3.7.3.zip

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