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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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[bioparser::FastqParser] error: invalid file format! #99

Open huandna opened 5 years ago

huandna commented 5 years ago

I tried use fasta file from nanopore to polish my genome of ecoli with racon v1.3.1 here is my code 

minimap2 ${draft_dir}/draft.fasta ${readpath}/reads.fasta > ONTmin_IT0.paf
time racon ${readpath}/reads.fasta ONTmin_IT0.paf ${draft_dir}/draft.fasta > ONTmin_IT1.fasta

and I get the error

[racon::Polisher::initialize] loaded target sequences
[bioparser::FastaParser] error: invalid file format!

Then I used the same fasta file to simulate a fastq file，and get the same error：

[racon::Polisher::initialize] loaded target sequences
[bioparser::FastqParser] error: invalid file format!

I used fastq as racon material without any problems before. this is my first time to use fasta file ,Is there anything different Between them? or is it because my genome is too small? Ecoli only has one sequence (4MB) and my fasta file is 1.5GB

thanks for your time huandna

rvaser commented 5 years ago

Hello Huandna, can you please paste here output of head -n 4 reads.fasta?

Best regards, Robert

huandna commented 5 years ago 
>9b5674d8-f03e-465c-9a6d-6a36ede08115_Basecall_Alignment_template nanopore2_20160728_FNFAB24462_MN17024_sequencing_run_E_coli_K12_1D_R9_SpotOn_2_66703_ch149_read134_strand pass/nanopore2_20160728_FNFAB24462_MN17024_sequencing_run_E_coli_K12_1D_R9_SpotOn_2_66703_ch149_read134_strand.fast5
TGGCCAAGCCGTTCAGTTACGTATTGCTGTTTTCGCATTTGTCATTGAAACGCCTTTCGCGTTTTCGTGCGCCGCTTCAGCCTGACTCCTGTACGCCACGGCTACACGTCGGTAATGCACGGTTCGCCACCAGACATATGGCCAGAGCGATGGCAGCAGTCAAGGCTACACGCGTCGGCCAACGGTCATCCTGCCTGATGCAAAAAGCTGTCTGCCTCACGAACAGATGTCTTTCAGCCCACGCGTTTGCACTACTGTCCTACTTCTCTGAAGCGGACATAAGCGTCTACCGGTGGAACGCTAAATGTTTTTACCCGTTGCAGATTCAGGGGTATCGAACGCCCTGAAGAAAGGCGCGGTCACAATTCATTTGCATATAGCCCCTCCGCTGCTCTCGCCACTACGCAGCGTCGCCAAGCAGGTCATCTAACAAACTATGCCCGGTAAAATGCACCTGGCGCCGGTGTTTGCAGAAACAGTTCCACCCGCGGTGCATACAAGAAGCCGCCCGCCAGCTTTTAATCAGTAAATGCCTGCCCTTCAATATGCCGGGCGACCATGTCACGCATTTTTCGACCGCCGGTTTCACCGCAAGGCCATCTCCACCGACGGCCGCGCGCTTGCTGCTCCACCTCTTCCAGCAGCTCGGCGATTTCCGGCGAGTCAGGAATGTGATGTCCGCCGGTGGCTTCATCCGCCGAGTACGTCACCTTGCCTTTCACGTGGCGCCAATACCGGTAGTGCTGCCGCCGCCGATATCCCTACACCGGCGTTGTCGGTTCTGCTGAATCCGCAACTGCGGTTGGCTCATCAGCACATGGCTCACTTCCAGTCCGGCAGATTCCCACGTTACGTGGAAATACGCGGGTCCATGCACGGAGAAATGAAGTCGCCACATGGCTAAACGACGACCGGTACCTCTCCCGAAGGCGTGTCGAGATGGCGACGAACCGTAGTGACGGCCGCGCCGAAATCGGGCGATGCCGTCGCGAACCATCGGCCCGGTCGAGGGCGCCGCCGCCCACTGGCTGACCGTCGCGGTCGACAACCATCGACACCGCTCGCAGGTGCCCGAATCCACCCCAGCCCTGGCGGAGATTCCGTCGCGGCGGCGTCCTGGTTACAGCGGTGCCGCCGTTTGCAGGCGTGGGGTGCGACCGTGTTCGTCGTGCCGCCATCTGTTACTCGCAAACAAGTACGAAACGCATCGGCTATACGCAACGACGCAGACGGACAAGCTGTACGCGCGCAAGTTGCCTCACCGGTTGGCGCGTGGTGATGGGTCATGGTGGTCCAGCCTTCCATAGCCTTCGCCCGGCAGCTGCACGATTCGTTCTTAACGTACTGTGGTATCAATAGCATTCTGCCATCGTTCCTCTTTTCGTGTTGCGCGGGCGCTACCGCCGTGGTGTATACCGATTCCACCGCTAGCGCAATGGCATCCACGCCACGTTGGCGGCACGCACGACGGTACCGGCATCCTCAGTTCTGGTTCACGGCAAACGGATGACTGCGTTGGACTCTGTGGCGCGTTCTTGCGGGTTTAAGGCCGGTGCCGCCGCCGCGATTTTACCTGCGTCACGTGTAGCGGTACGGCTGACAGCGGTACGCGCGCTCGTCGATGGCCACCCGCCCACCAGTTTGCAGCTGCTGCGCCGTTCTGCGGTCGGCACCGCGCGTGCTGGCCTACATCGAACACGTAGTTCATCGGCTGCACGCGCTATCAACAACAATCAGTACCTTTTCGTCGGCACAAATGATGTTGTTATCGAAAAGCGCTGACGATGGACTGAGCAGCACGGCAAGTCGGCGGACACTCCACCACTACCGGCGGGTTGGCGCGCCTGCGGCATCGAACGTACAGTGTGTTGCCGCCGCTTCTACTACCGCTTCGCCGCCCGGGGTTACCCTGCTGGCCGATACCCGAAGCTTGAACAAGCGTTGCGCGGTTTCGATATCGGGTGCCCACCGCAATAACCAGCGTAAGTTTTCCGGCCCTACCTGCGGCAACAATCGCACGGGTTGAGCAGCATGTCGCCGCTACAGAACTTTCGCCACCAGACGGGGTGCATGACGCTGTTGCCCGCCGTCAGGCGCTGTCGCGTTGTTAAGCTGCGGTTGCCAGGACAATCACCGAAAGCCACCACGCCCGGTGCGTTTTCGGTGAGTCGGAGGCCGTTGTCGCCAGTCGCGCACTTGCGGAGAGAGCACTCAACGCACAGGCCGCACTGCCTGGGCGACGTTTCTGGTATCTTCAACACGCCCCATGCCGGTTTCACTGACGGCAAGTTCCGCTAAATCTCTGGCGTGTTTTTCGCCGCCGCCACGAATAGCAATGGCTAACGGCACGTACCACGCTTTTAGCCCTTGCTGAGCGGCACGGCTGCCCTGCGGCGTCATCGAGGGACGCGAAAACGCCCATCTCCGCGAACGGCGGCGGCGGACGGCGTCACTGCTGCATTTTCCGGCAGTACCGCTGCACCTGTTCCATGTCCTGTGATTCATGATGTTCTACCTGCGCTGTTGGCCAGAAAGTACCCCGGCCGCGAACACACCTCATCGACAATGCCAATCCGCACAGATGACCGGTGACGTTCGCTTTATGCGCGCACGGCGGGCCAGAACTACCACTACCAATGGCACTACCTCCGGTTCCGCGCCGTATTGTCGTCGCGACGGCACGTACCCGTCAGGATACCTTGTGGATCAATCGTTCCACCATCGCAATTTGTCGTACGCCAGTCCCGCACGTGATGGCGTACGGCCTGTAAACTGTCCAGTGACGACACCAGTTTCGCCACCCGCCTCCGTGGCGTAGCATTTCAGGTAAAAGCTCCCCCTACCCTCCGCAGTAAATGAGAAGCGTGACGCCCAGATCGACGACTCCGCACAAGTGATTACAGAGTTGCTGCTATCGCCTTTCGGAAGGCGATCGACTTCTTCCGAAGGTCGCCGACCTGCCTGCAGACCGCGAATAACGTGTACAGATACCACTTTCGCCGTACGCTGGTACCTGCGGCACTACATCCGGTCGCGGCACAGGGCTGCTGCTTATCACCACGAACCATGGCGAGTACACGGCCGCCGCCAATCGCCTTTCCAACCAGCTTGACGCGCACCCGGCTCCACCGGCATCGCGTCAAGCCTCAATCAGTGCGCTTGGGCCCGGGTTTCGTCATTTCTAATGCTTCCTGTACTTTCCTCTTTGTCGGGGTCCAGAAACGGGACCGTTCGATTAACCAGATGTTTGTAAACTGCTTTCGCGAAGTTCACTTCTGGTGAGCGCGCTTTGCTACCACCAACGCCAGCTCGATAATTTCCTGCACTGTGCAGCCGAAGATCGTGCATCGGCGCGCCGTCCGCTTGTATCAGTGGCCCGGCACGTATCCGCCAAGTCGTTGTGCGATTTTGTAACTGTCTTCCTTCCAGCGACGGAAAAACATCCACGATGACGCCCCTTGCCCTGTAGCAGGCTGGCGGCTTTTGCGCCGCCGCTTCCGGCGCTGGCGGCGGCGTCAAGCTGTAACTCGCCATCCACCGCCGCTGGAGCACTCACGGACGATTTCTGTCGCCTGCTGGACGTTATATGCTGGGGTGACAGGCGCTACCATTGCTGAAAACGACAGCATCGCCACGCGCGGCTCTTCTCCGGTGATGGCGCACCGGGTTCTACCGGCACTGGCAAGCGCGATATCCGCCACTTCCGCCGCCGTCCGGCTGTGGCACCGCTACCGTCAGCAAGCCATGACGCGCTGTACTGTGGCAACATCAGGAAAATGAAGGCGTTTACAGCGGCTGCAAGCCGTCATGTCCGGCACGCAGCACCTTTACCGTGAAGGTTGCCACGTACAGGCAGCTCGCTTTACCGCTGACCATTGCTGCACGGCGAACATCAAGGTCGGTAAGTTTTCCAGCGCATCCGGCGGCGTTTTCGCCCGCGCGGGCCTTCAAGCGATAAACAATTCTTCCCGCATTGCGAGGTTGCCGCAGATCAGCTCACCTGTAGCCCGTCCATCCGCCACGCCGAGCTGAAGCGCAAGCGGCGAAGTTCAACGGGCGACCGGTAGGCGTTGCCAGGTGCTGTTGATGTAAATATTGCGCGGCTTTCGGCACGTTGGTCGGTCTAACGCATCCGGAAAAACCCTCTGGCGGGCGCTCCTGCGCGCCAGTTCGACAACGTTCAACAATCATTGCATTTCCCCAGTCGTTGTTGGATCTACTTCACCGTTAGCGGCTGCTTCGTTACGCTCAAGATCATCATCACGTAGACCGATATAAAGAAAGCGGTTCAGCGCCTGCCATCGAGCGTAATGTCACCGCTGCGGTGACGGAAAGCCGCCACTTCTGGTTTCCAGTTTCCACCGCTGGTGCGTAACAGGTAAACAGCGCAGCATCGCGCCCGTGGCTGGCTTCCCGGCACCAGATGATCGTGGTCGAGATAGCGCAGCGGCTGATGAAAGCCGTGCGAATCTTCGTCGAAAGCCGACGGCAATCGCACGGCGGCGGCCGGGGCTTCCCCAGCGCATCGGCGCGCATAATGTTGCAGGCGACATCGCATGGCCGGCTGCCACGGTTCCGCCAGTTCGGTACGCCCTGCCAGCGCAATGGTGCTGTCGAGAACCGCGCAGCAGACGCGGATGTCGCTTTTGCGACCATTTTCACCGCCGACAGGTGAGTGGCGTATCCGGCTTTTGCCACCGGCTGGCGGCAGTTCGCGGCACGCCTGCGGATGATTTTCATCGCTACTGGTCAGCCCGCAAGACAGGCTGCGGCTGCTCTGTTCATCGTCAACAGGCGGCCTGCGTCAGCCGGCACCCGATGCGCAGATGGCTTTCAACTCCCGGGCAGAGGCGTCAGGCGGCGCTGTCCGCAAGGAGGGCTCTCTGCGCCTTCGCTGTAGGCGTATGGATTCCGCTCTTAGCCATGCTTCGGTGATAGAAATGCTTTCGCAGGGATTGCCAGTTAGCCAGCGGGCGACGCCTACAAGGCTTCACGCTGGATGTCGTACCAAATTCGATGCACTGGGGCCTTTCGGGTTCAACATCCGTCACCTGCGCACGGCGTCATGGTTTGGCGCTTCGTGGCGAACATGCGGCTCCTTCCAGCACCATGTCGATTTCGTCGTAGTTCAGGGTCCACGGGAAGAATGCGTTCTCCCACCGCCGGCTCCGGCAGCCATGTGCTGCTGCCGTCGTCTCCAGTCTGGAATCAGTCAAAGCCCACGCAATGCGGCTGCGCCGTCAGAAACGACCGGCGGCCCGCTACTGCCATCATCACTGGTACCGCCTTTACCGGTCACCGATTTGAGAAACTCCGGCTGCATGCGCCCTGCTCCGGCTGTTTTTCCTTCATCACTTTTCCATCAGCTGTGCGACCGAGCTTTCCAGTAAGCTGCTGGCCTTCCGGCGGCTTGGCGCTAAGACGTATTCGTTCCTGCGGATGCGCTGGCTTTCCGGTTTGTCGGCTGGCACGCTGGCGGGCACGGACTTCGTTGCAAGGATCGATTCATCACATTCGGTGATGAGCT
>bb0023d4-6275-4db0-bc74-6fcdc0ca5217_Basecall_Alignment_template nanopore2_20160729_FNFAB24462_MN17024_sequencing_run_E_coli_K12_1D_R9_SpotOn_2_95274_ch311_read1665_strand1 pass/nanopore2_20160729_FNFAB24462_MN17024_sequencing_run_E_coli_K12_1D_R9_SpotOn_2_95274_ch311_read1665_strand1.fast5
GGACGTACTTCGTTCAAGTTACGTATTGCTGTTTTCGCATTTATCTCGTGAAACGCTTTCGCGTTTTCGTGCGCCGCTTCGGTACCGCGCGGCTCTGCGGCCTGCATGTCATGTTTTGCCGGTACGCGGCAATCGGTGAACCGACTTCCGCATCATCTTCCGCAAAATACGTTCATAACATTCACGGTAGATATAAAGCGTCACAATACACCGCGCTGCCCACTTACTATCGTTTCTAAACAAAGTTTTCATCAGGTATTCTACTGACTTTGTTATAAGTGTTAAGGTAAAAATGGGGCTGGTATCAAAGCGCGCTCGGTGCGCTGGTAGTGCTGTTGATTGGTGTTTAGCAAAAGCAAGTATTATATCGCCGGGCGTTCCACTTTTCCCGACCTTTGCGCTTATCGCGCATTATATTGTTGCCAGCGAACGCGGCATTGAAACGCCGCAACCATCATTTTAGTATGGTCGATTATTCCCTATTTTGTTTTGTCGCTGGTATTTCACCGGAATGCGCTTGCCGCCGCTTTGTTGGTTCTGTTGCGTGTTGGGGGATAAGCGCATGGTGATTATATGCTGGATAAGCTGCATTAACACTGAATGACGACCGCCATCAGTAAAACTGCGTCCGGTGACAAAAGCAACTGATAAGTAATCGACGGTCGTCACTTCTTCTCGCCGAGCGGTTTTCATCAGTGATTTATTCGCGCCTGTTGTCGATATTCGGCATGTCATGTTCGTGCTGGATCGGCAATGGCGCAATAAGTACTCACTTCCGGTGCCTGCTGCGAACAAACGAGCGGAATCATATTATCCAGTGCCGCTTTATAACGCGGCATACGCAATATGTTTGTCCTTCGCGCTCCACCATAATCATTAAGTGAATGATATCGCTGGCGGCGTGTCCGTGCCACCAATGACTTTCCCTTGCATGGTTGAGCAGGTATGGGGTATTAACGTGGATCTGCATCGTACAAGCCAGCCAGTGGCGCACCATTTTCCGCCATCACGCACTGGCGTTATGCAAAACGCTTTACGCAGACCATGGGTGCTTTTGGTACTTCATCGGCAAACGCCATCACACACCGTCGTTGGTCGAAAAATCAGCCTGTCACTGCGCACCTGCGTGTCAGTCATCAATGGCTGAATGGTGTGTCCGTAGCTGACATCACCGGTTGCCTTTTGATTGTAAAGTACCGTACGAGGCGAGGCCGATGCGACGACCTCGCCAGTAGTATTGAAAGCGGGCTGGGTTTACCCATCGTTATCTCGCGCTACATCTGTCGAGATAGTATTATCCAACATCAGGTCACCAGAACTGAAAACAATGCTGCTGCTCTATCACTTCCTTCTAACAGTTAGTATCATAGGTATTATACATTTTACACCTGTAAAACTCGCAACAGTACTAAAGCTGCTGAACTTTTCTGCTAAAATACGTGAACCAAAGCATATCTTTCCTCGCTCCTCATCACAAGCTTCAGCACCACTATGTGATAGACAGGTGCAGTACAACAAAGCTGCCTGCGGCTCGAAACTCGAACAAAATCCTTCTGAAATGTCCGCTGCTGCAATATTATATCAGAACCAATCAACAAATAAAGCTAAACAAAATTACTACAAATATTAGTCACTTTCTAATAAAAACGAATACTTTGCTAATACATTCTTTTTCATCTGCAAAATACTATAGTAGCGAGAACAATACTACTACCATAATGAATCTGCTAAAATACCCACCTAAACAAGCTATCGCTCCACTGCTGTAATAATTCTATAATCCTCCTTCCCTATCGAACCATGACAACAGGTAAGTATAATTCAGAACATTCCTATTAGCAAAAGCGCGTTACCAACAAGTAAACGCCAAACGAGAAAACCGCGCAGTGTCGCTTTACCAACATCACGTTTATTACGCGCACGCGCAGCTGCTTTCGGCACCTTCCCGCAATGAAAACCCACAGGGTGATCGCTACGTGTTTCACCCAATTCCCAACGGGCACGCCAGTGCAGGGTCGGTGGTGAGATCGTGAGCGAAGGTATCCGGTTGAACATCCTCATCCAGCACAACAAACAGGCCAGCGGCAACAATTTTGCCGAGTCGCCACGAGGTTAATACTGGCAGCGGTTTGCACCGCAGAGATCCAGCAATCTGTAAAGCCGATGCACCGACTATCGATTACCGAGGCCAATACCATCTTAAACGAGCACGCAATTCCGGCGTGTCCATGCTGCTGCAGGCAATCACCAGATAAGGTGGCGATGGCTACTTTTACAGCCAATATCCCCATAAGGAACAAAAAGCCGGTGTCGCCAAACCTTCGCGAGCATGGTAAAATTCTACCGTCAAGTTCAGGACGAATGCGCGTGAGATCAACATAAGCAGGCCAGCAATAAAATGCCAGCGCCAGTATACCCAACCGATAAACAGCAGGCACGCCGGGCTGGCAACTGCCACTGTATTTTGCGGCGAACTGAAAACACCGCATAACGTGAGCTTATATACCAGCGCGGTAGTGCGCTCAGTCCCAATTTCTTTCCATCGACCAGTGATTAAACGTGATGAAAGAAATAATATTAGAGCAAAACGCAAAATAGGTTGCCACTAAGCACCAGAGATTTTACGAAGATGTGTCTGCATGCAATGGTCGCGAAATTGTGACTAAAATGCGAAACGGCATCAAGCCGCCATAGGGCTAACTGAATAGTTGTTATACAGGTCTGCTGCGCTGACTTCAGGTTGTACCACGTTCTACTGGCAGTGATATTAATGTCTGCCTACTTCTTCGCAGCGTTTCACAACCTGATAGAGAACTTCGTCATATTGCCATAATTGCCAGAAAGTATTGTGTATCCAGGCGAGACCATCATCACTGCAGTGCTTTGTTCAGTTCTTCGACTTTAGTACCATCCGAGGCGTGACGGTACATGGCACGCCTGCTGATGACTGGGCTAGCGACGACTTCAGAACTTGGTGATGCGGTAGTCGCAACACCGAGATCAACTTTCTTCGCGGCTTCGCCACCGGCAGCTTGAAGCTGCACACGTCCTGCTTCAGGTACCGGGACATCCAGGCTCCTGAACGTACATTTCTGCCATCTTTTATAAATGGGCCAATATACGCTAATTTACCACCACAGTTAGCATCGGTGACAATGTAAAAAGCACCTTTCACTTTACCACTTTGGTGATAGCATCGTGACTTCGCTGGCTGATAAAGCAAGACGTGACCGTGTCAAGCGGTCCAATCAAGCTGTAATCTTTCGGCAATTCACCATTAATACGTTACCTGTTCTTCTGCTTTTCAGCATCGGCGCAAGGTCGCGACCACACCAATTACCGCTGTTACCAAAATCCGTCGACAACATAAAGGCGGCACCTTCTTTATCTGCCGCGACAGCAGCTTTCACCGCTTCATATGCAGCCGTAACCGGTAGCTACACGGTCAAGGTTTAACTCGCACTGCCGCTTGCTCCGGTGTCAGTTCTGTTGTTGCACCGTTAACAGAAATACCATAGCAACGAGTACCGGCTTACCGAGGAGGTGTTCTTACTTCGCCAAAAATAATCCTTCGCCTTGCTAAGCAGTACTGGTATTGTGCTGAAAACGTGGCTGATGTGCATTTAAGCGGTGTAACTGTCCGTCATTTCATATCACATTCGCAAGCAATTTATCCTGCTCAAATGACCGTCTATGCTTAAAACAACCGTATCAGCATCGTACTACTGAAGCAACGCTGGTATATAAATTAATTTATGTTAAGTAGTGGTCGTGCCGCGAGGCGATGTCTCACATTTACCGACCGTCGAGCAATTATCCAGTCTTTATCCGCGCGTTCTAAGGTGTTGCTCCACTATCACGTGAATCGTTGTATTTTGCGAGTTCACGCCAATACTATTTTAGCGCTAGATCACGGTATAATTTCCAGTACGTTATGGGCGTTGTTACTAGTGACTGCTGAAATGCTGTTGCTCGTACGCGAACGCTGTGTGTGGCTCCTGACACAAACCGCCATCATCTCCGCCGATGGAGAATATCATGCAGGTGGCATACCAGAAACGTTATAATAAAACCCGTGTTGCAGCAACACTTTTCAAAGCTCGTGGGTGCTGCACTGGCTTGGGTTTTACCGTCGTAAAGCAGCGCGAGGTCAACAACAGGCTGACGTCACTTGTTTGTGCAAGCAGGCATGAAGTATAGAAACAACGTCTGGCAGTCAGAATCATTCTGAAAAGTCAATACGCCGTTCGGAATGATAATGCGTTACTGAATCACAGGACAACGCTGGTGAAGTTTATCTGGCCTGTACACCAATCCGGGGTAATACAAAACTTTTGCAGAACGTAACGTGACCGTGATAACGTGGACTCTGTGCCGCGTATCTCCACGCACTATCCTTCTGGTTACTAACTCAATGCCTCACCGGTTATCGCCGCCATTCTTAAAGCGGCATTTGGGCGCTTCTTTACCGAACAAATGCTGCGGCCGGAAAATTACCACCGGCAAAGTGATAGTGGTGGTGCGGGTGTTGCAGGTCTGGCCGCCATTGGCGCAGCAAATCTCAACGCGGTGTGCGTGCATTCGACACCCGCCGGAAGTGAAAGGCTAAGTTCAAAGTATGGGCGCGGAATTCCTCCGGCTGGATTTAAAGGAAGCTGGCAACGGCGATGGCTGCCAAAAGGAAGTGGCCGAACGCGCGTTCATCAAAGCGGAAATGAACTCTTGCCGCCGAGCAAGGTCGACTATCGTGTCACCACCGCGCTTGTTATTCGAACAAACCAGCGCCAGCTGTACCGTGTGATTGACTCCATGAAGGCGAGCAGTGTGTTGTCGACGGCGGCTAAACTGAATACCGATGCCGAGGTAATCTTCACTACGGAAAATGGTGTATCAAGTAATTGATTGCTCACCACCGTCTTCCGAACGTCTGCCGACAATCCCTCACAACTTTACGGCGCACAAAACCTCGTTGGCTGAAACGTGCAAAGAAAAGACGGCAATATCACTGTTGATTTTGATGATGGTGATGCGGCGTGGCGTGATCCATGCGAACGAAGTACGGCCGGCACCACCATTCGGTATCAGCGCTCAGCCACCAGGCAGCTTTCACTGGCACCAGAGGTGAAAACTGAGAAAAATATTACCTGCTCACCGTGGCGTAATACGCGTTGATGGCAGCAATCATTCTTTTGGCTGGATGTAACGCGCCGGAAAAATTCTTGAGCACCTACCGTTTTCGCGCGGCCTGCGTTGTCGGTGTACGTGGTGTAAGAATATCACGCGCTGCATACACCGTTGATGTCGTCACCAACGCGTTCAGGGATTGTGTTGTCGAACTTTTGTTGCAGGTGGCGGGCGGCTGGGTTGCTTTCCTTAGTTTTATCGCGGTGCTTATAGCCGGCGTGTATTTTCGGTGGCTCACCGTGACTCACATGTCTTTGAAAATGTTCCTAAAAGTGAAATTCAGCACCGCATGCGGAGGATTGGTGCAGCTACTTATTGTTGCCACCGTCCTGTTTATCTTCAGTCTGGCCGGTCTTTCGAAACATGACGTCTCGCCAGTAACAACATCTTCAGGATATGGCGGTGCGTTATCTGGCTCATTTTAGACCGGATACGGGTAATGTTG
rvaser commented 5 years ago

Aren't you missing > before each sequence name?

huandna commented 5 years ago

I am sorry it is so long ，I am sure I have ‘>’ for each sequence

rvaser commented 5 years ago

If the above snippet is the result of the head command, then you are missing >.

huandna commented 5 years ago

oh,Maybe the problem is that the results displayed on the web page are different from those in Linux. I will find a standard fasta file to test again

Thank you very much huandna

rvaser commented 5 years ago

The raw text has them, my bad :) Can you run tail -n 4 reads.fasta?

huandna commented 5 years ago 
>bbd2133f-bda7-4058-a4d0-ef6c5ede463d_Basecall_Alignment_template nanopore2_20160729_FNFAB24462_MN17024_sequencing_run_E_coli_K12_1D_R9_SpotOn_2_58342_ch312_read958_strand1 pass/nanopore2_20160729_FNFAB24462_MN17024_sequencing_run_E_coli_K12_1D_R9_SpotOn_2_58342_ch312_read958_strand1.fast5
TGGTAGCCACTTCGTTCAGTTACATATTACTGTTTTCGCACATTTATCGTGAAACGCTCGCGCATTCGTGCGCCGCTTCGAGTGATTGCTGGTTGGCCTTCAGTCACCCAATAACCACCGACTACCTCCGCGCCTCGCGAGCATGGCAGTGGAGCCGGTGGCACATGTTGAGAACGGCTCGATCTACTGGGTCGAAGCCCGGCGCGCGCGCTGGTGGCGCGATACTAAATCAGTTTAACACGTCTCGCTGATGTGCACGGCTGACTTCTGGCGAAGTGATTGCTGCCTGTCGGTGGTTGTATCACTCCTTGCAATCCGGGCATAAAAGCGCGTCGTCAGGACGCGCTTTTGTGTACTATGTACTTCAGGTATTCACCCGGCTGAGCTTCCAATTCGTTTATCCAGCGGCGGGTGGTCGCCTTCAGACAACTCACGAGCGATTTGACTTACCGTTATGCAGAGAAACCATCATGCTGGTTTACACTTCTTGCAGTTCACCAGCTGGTTTCAGGCGGCGCTGCAGCATGACATCCATTTTCTGCGACCATAGTTTGCTGAGCATCAGCGCCAAATTCACGACGCGAGAACCACGCGCGGTGATAATACTCGCCAAGGCCAAGCCTGGTTCAAGGCCGTTGCAACACCAAGTAGATCAGCAGGTTGCCGTTGCTCTCACCTTCATCACGATTTCCGCCCGCAAAACCCGCGGCAAGCTGCGCCAGAATAAAATAAAAATAACGAGGTGTTCACCGCCCTGAATCAGCGTCCGCAGGTGACCATATCACCGTAGCGTGTGGCTGATTTCGTGAGCAGTACCGCCTCAGCTCCGGGCTCTCATGTTCTGCAGCAACCGGTGCTGACATAACCAGAAGGCATCACGGCGCGCACGGTTGCAAAAGCGGTGTGTCCGCATGGTAGAATAGCCGCACGCAACGTCCGCGGCAAGAGCACGGGTTGCTGGTATTGACCAGCCAACGTTCCCTTTCGTTACGCGGTTGCTCAATCACTTCCCCGCCAGATCGTATGCCATCATTTAAGACCTCGAAAGCGAAAACGAAGGAACGCCGCAAACGAACGCCGAAGCCGCAATCTCAGCCCTGTTGCTGCTCATTGCTCCTGTCCGTCAAAACACCAGCCAAAAGCAGCCGTACGGCGGTTCGTTGCTTGAGGAAAACGCAATTCGCATCCTCGCCCTCTTTTACCTCAGTTTAACAAACGCCTGTGCATGCGATACCCATCGTATGGGTTACGCGACTATTTTCAAGTCTAGATGATGCGTAAGTACCCCAGAAGGTACAACATTTTGCTCTGATTTACGGCATCTTGTCGCTGTTACCTTCGCATCAAACTGTTCTTGTGCCTGATTGATATTATGACGGGGAGCAGGTTGTTCCGCGGGTCTGGCTTTTCAAACTTCGCCCGTCGAGTGCGATATTCCCGTCTCATCAGAATAAAGATCCGCTCCACGGTAATCTTTCGGTAGATCATCCAGTTTCTTCCTTTCCAGTTTACCTTCGCGTTTAAAGCGTTCGTTTCAACGCGCCAGACGCGTCATCATCTTCGCCTTCTCTTCTCCGCTTTGGCGTAATTCAGAAGAAAACGATATTGCGCTTGTCCAGCCCTGCTTGTTGAAGCCGCGCGTCCTTCATGATGTTTCTGGAACTCAAGTCTTTTCACCCGAAATACGCGCATTATGTTCGCGCTCCGGTTCCAGCCGTTAAATCTCCTGTTCGCAAGTCGCGGCATCCAATGCTGTCCAGCAGCGCGTTATCTTCAAATTTCTCCCCGTTTCCGTTCTTTACAGCTACCGTCGGCATGATGATGTGGTACACTTCGTTGCGTACTACCGCCATTAACGCGATAAATTTCTGGATCGACGCACACTGCGAACCTTAGCACTAGCCCTTCAGGACGTAACATCTGATCTATGTCTTTACGGTTCAATGAACATTGCGCTGAACAGTGCCTTTGCCAAGCATCGGTTCACCTAACAACGCGACCATATTCGCTGCCGCAGCAAAATTTCTAAGCCAAGCACTGAAACAGTCAACCAGCACCACCAGCAGGCCTTCCTGCCTGAAAACCTGTCCGTCGGTATCAACTGTCTTCACGAACCGTTGTTGCTCGCGGGCCTGAACAATAGGACCCGCAGGAATAAACAGACCGGGAAACGTGCAGCTTCGGTCGCGCCCCACCGCCGTACTGGCACAAGTCCGTGATGACGCTACTGACATTCTGTTTTTCCAGTTTCTACCGCGGTGCGCGCTGACATCGTCTGTCAAACCCGCAAAGCCCGGAATATCGCGCACGCCGACTTTCTCTTTACCGACGGTCTTCACCGACATTTGCCGCGCAGTCTTCAGAAACTGAATACGTTCGGTCAACGTTACAATACAGGTCATGTGGTCCCGCTACCTAACGGGTAAATTTCCAGATGAGCACTGCCCTTCGGCCCTTTAATTAAAACCTTAACCACATCATCAAGACGCCAGCCATCCACGTCCTTAACCATGTTACCTGTTTGACCAACACAAACAAAATTTGTCACCAACGCTGACCACTTCTCTTCCGCTGCGAATACCTGCCACCATCCAAGGTGATAACGGTGTAGTGTCATCCATTGCAACTACGCCATACCTTCCAGCAAACTCATTTCAGTATTGAACTGTTCGGTATTACGCGGAAAAGAATAGTTGTAGTATAAGGTCAATTCGCACAAACGCAAATCATGCCAGCGAAAACAGCATCTTCGCTGTTGGTTTGCGCCAGACGACGAATATAGCAAGTATGGCGGCAAGTCAAGTTTCCACATTTCTTTATATCCGTTTTCCTGTCAGCTTCAAGCTTAACTCGTCAGGTGACTTTACTGTCCCAGCGCGTTCAACTCAACCTCGTTTCGGCGGAGGCGCGCTGCGGTCAAGGTTATAAGTGTCGTTGGTGAAAATCCATCTGGCTTTCAGTACCGATAAAAGCGTACTGGTAACGCTCAAGCAGCGCTTTGCCAGGTGTATAAGATCTGGCAAAAACGTCGAGTTTGCACTGAACTTTAATTCATCACCTACTCGGTTTCTTTCGCGAACTGTTCTTATCGCTTGCCAGCAACACGTTGTATGGCTGTAATCGAGCAGGAATTCAAGTAGCAGGTCTGGTGGCAATACCTAATCGAGTCGGAGCAAATAATAAAACAGGTGAAGCGCGACGTTACGCTCACCATCGCATGCCGTCTCTTCACTTTAATACCAGGGTAATCAGCACGCGTATCTTCTGCTGAAAGGTCTGGCCTACTGTACAAGCAAGCCTTCTTTGACCTTCACTTTATGTTCATGCGGCCAGCACCTCCGTTTAAGAACACCAGGTGTTCTGCACGCACTATCAAGACATACCAATTCGCTGGACGCGGACGCCGTCTTTGGTGATTTCATACGGTGGCATCATCGCGGCCCACTTCACCTTCAGGGCTTGTCCGACAGTCAGAAGCAAAATGTCAAAAACCGGGGTGTACTGTTCTTCACCCGAGAGTGCACTTTACTGTTGGCGCTTTCTCTACCGCTTTTACGCACGAGTTACGTTCAACGCCTTCTTTGCGGCGTGGCGTAGTCAGACGTAGCTTACGTTGCAGCACGGTGCGTCTTCTTTCTCACCAGCAATTGCGGCAGCTTCGCGTTTCGCTTGCTGTTCTTACACTGTACTGGTACCTTTCGCTTCTTTAAACTGCTTGCGACATGCTCTACATATTGCTCATCCAGCTCACCTGGGTTACCGTCAAAATCGAAACACGCGTTGCACCGGGTTTCACTACCGTAAAAATACGCCAACTCTCGAAGATATATCCTTAAGGCGCCAAGCGGATCCTGTGCGTTTACTCCGAGTTATTTCCCAACAACGTCGACCAATCCACAAGAAAAATACCAATTTCAACGGACGCGCTTCACCTTCCGCACACTAAACAGTGGAAACGTTCAGCTTCGCTGCAGTACTTCTTTACTACTATTCAACTTAGGTTGATTTTCCATGAAATTCACGATTACAACGGACGCGCCAACTCCACTTGCGCAAACGAACAAGCGTCGTATAAGCGCTATCAATGCATCTTCGTTATCCGTTGATTATCCGACGCTCTTGAAATTTTGTAATCCGTCGTTGCAAAGCACTTTTCGGCTGTACCTGGCTGACGTAAACCTCATCCTCGTCATAAAACGGCAAGACGGTACTATCGATGTCGAAACACAATAATCTACACTACCACCGGCGTAGAACAAATTTCAAGGGTACTCGCCACCTCCACAGCTCGCTCACCCGTCAACGCCGAACATCCTCGATACGCTGCACTTGGTGCGGGCAACCGCAGTACCCGCACGCGCGCCGACAGGTATCCGGACGCTGACAATTTGCTTGCCCTGAAAATGGTCCAGTACCAGTGTATCAATCCTCAATGCCATCGCATGCCCAGTTGTATGTCGGTGAAGACTCCATATAACAACGCCCGCACTGAGTGTTCACCGCGTTGCGAAAAGCGTTTCTCCACCGCGCATTAAATCATTAAATACCGCGTAAATTCTGTTTGTTCATTATATAATCACTTGGTTGTCTGCCACACCAGATCCGCAACCTAATACGCGTGGCATTAAATACGTTGTCTCCGCGTCCTTCCATCTGGATTGGAATTAATGTTAATTCTTAACTACATTTGGCACATCATAGCTCTTACCCCCTGATACGCAACAAAAATATGGTAGAGGGCAATCAGCGAGAACTACCGCAATGGTAATTACCAACGGTACCCGCAATGCGACGCCTGTTTCGCCTGCGGTCATTCTCCATCAAGATACCTATTGTGTCCGCGCTGTCAGGCAAGTATTCGCTGACGGGCACGACTGGTCGCTAACGCACGGCGGCAATGGCGCTTCTATACTATTGCTTATACCGTTTACAGGGGCGACCGCTGTTACCTATATATCTGGCTGTTGCATTCGTGACGCCAACGTGCCTGCAAGAGCATCTGGCGCAAATAAACAAGACGTCGTCGCAGGGTCGATGGTCTTTTTCTGCGTTATTGTTTTACTCATTCTAATGACCTCCACCTGTATTGCTCGTTTGGCCAACCGACTGGGAATAATTACGTCCACGAGCTACTGATGCCCGGAAACGACTTAAAAATTGTGTCTCGTATCACGGTGGCATTAGCATTGCTTCTATAAAGTACAAGATTATACCCGCGCCTCGGGCTGGTGTCGCTTGTTCTCCACTGGCGTTGGTGATTTCTTTGTATTGACGTTGTCACATCTGTCATCAGCAGAAGAACTGTGAGCGATTTATCCGCGAAGCGCCCGCTACGCGTAGGACGAGAAACTTCAGTGTCTATCTTGGACATTTACCAGCTATCGAATCAGCGTGGTCGCTGCCCGCGTTGCCATATCCGCTACGCCTGCGTCGCCGTCATGGTCTACAAAATGCTGGGCGCTGTTGGCGTCAATCGTTTTATTGTTGCCTACTGTAGCCTGTTGCCTCTTCTATCATTTATCAGACGGGACGTAGGAAGGCCAATTCTTTCCGGAATTATGTCAGCCGCCGTAACCTTGTGCGGTTAGGAATCGTGTTTATCCTTGTTCTGGTACCGTTTACTAAAGTGATCGTCATGTTCACTTTGCTATTTGAGCACCCCATTCATTTCATCGCAGCAAAGGTTTGCCCATTCTGTTACTGCGGATATGGTGAGGCACGGATTGGTCATGGTCGATCTCGACTGTTTGGCCATATCTTGCTCCTGTCGCTGATTAATCGCGATCAGATCTCGCTTTACTATGGGACCGGCCGTTTGTTTCGGCACCGGCAGTAAGGTACGACTATTCTTGTGGAATGGCTGGACAGCGCTTACTTTAGGATGCATGAGTCAGGAAACGCCCGCTTCGACGACTAGAAGCGCAGATTAAAGCTCCTTGCCATATCTCACCTTTCCTGTGCTGCACCCGATTTCATCGCGCTAATGATTACCAGTTAGCTGGGGTGGGACAGTTATCAGGACCGGGGTATGCCGTCACCATCGGCTATGTCGGCGGGTGGTATGTTCGAGCCGTACGCCTGTTCGTTGGGGCGTTGAAGTCGGAACGGTGCAGGGATATCAGCCTCAGCGACGCTAAGCAAGACGAAGTCGGTCAACATCAGGTCAATGCAAAGATGCTGCGGCGAAAGAGCTCAGTTCGGCTGGTGGCGCAAGCATCGTTGAGTGTCTCCAGGCTGCTGGACACGCCCTCGTCCGGTGGAACTACTGCTCAGCAGTGCAGGTAAAAGGTAAAAACGGGATCACGTGCACTCGATACCCAACGAAATATCGGCTGGACAATGGCGATCTGACGATGATCACCTGCAAGCCCCGATCTCCCAACTGAACGGCAGCGGTTCATTGGTCTATTTCCGCAAAAGATCGGTGGGAAAAGTCTGCGACTATGCCATCATCCCAACAACGAGCGTGGTGGTTGATAATGCGATCAACGGCGTTTACCGATCTGGTGAAAAAGTAGCGTTTCTGGGAGCATTTCCGGCGTTGATACCAACGTCGGTATCGGTGGCGCGAAGGTGAAACTGGGCTTGGCGGCACTGGTTGCTGATGCGGTGCCGCTGATTCACCAGAAGAGTCGAGGCTACCGAGGCGTCTGCTGGTCTGTGTGAATCGGCCCACAGCCAGCGTGGCGTAATAATGAAACTGGAACACCGAGTGGGGCCGGATTAACCGCCGACTCGACGCCGTTGTCATATCAGGGCTGCGGTCGGACGGCTTATTCGCTGGTTAAATCCGAGGTGGTGATCTGCCGAAATGACCGTTGATCCCAGCGTCGTTACCTGCTTCGTGAAAATACCCTGGAGTACGCAACCCGAAGTATCCGCCCAGCGATGCTATCTCTTCCGCTGACCAGCAAAACCTTCACAATTTCCCGGCATTGGCGAGCCACGCAAAAGTTCGTTGTTGACGTACGAGCGGCACTGCTGCATGAACCTGATGTTCTGACGCCAGCCCTGGCCGCGCCGGAAGGTTACATTATTGATGCGGGTCCAGCGCTCATTCTTCACGGCGTGCAGGTAGGCGGGTGTCGATCGTACCGGCTTTCACCAGCAAGGCGTCACCTTTACCGTAACCATCGAGCCTCATCGCGAACTGGTAAGGCGTTAACAAATTCGTCAACAGCCGTGTCTCGGTGAAGGTGGGCACGGATGGTGAGTTCGTACCAGCGCCTCAAGATGGATCAATGGCGGGATGCGTATTCACCAGAGCGATAAAGGTGAGATGAAAAGCCAGCTATCCTGCTGCTGCCAATTTGGAAAAGCTGGGAGAACTGGCCTTGCTTGTTACCCCACCGCAGCAAATGAGTTGAGTGCAAGACCTTGCCGGATGTGTGCAGGCAAGTCGGTAGTGCTGTACCATAATTTGGGATTGGTGAAGTGATTACCGTGCGTCCGCGAATAACGCGTTTGATATCTGCATATTCGCCGGGTATCGCAACCTTCGACCAGCAATAACAGCGTGTTCTGGGCGGCGGGGCGAAGTTCAGCGAATGGTAGTGGTCTGACCATTGCAGGCATCCCGCTCAAACGTTAAAGAGCCGTACTTCGAAACAACCTCCAGCGGTGCGGCGCCGGTCGCGTAAAGGCGATAAGCGTATTCTGTCGCTTCCCGAAACAGCAGCCCGTGCGGTTGGCGGGCAGACCCACGCTTCACGCTGCTGCCGGGCTTGGCGGTCATGCCGAGATTCGCTATCTCCGGTGACCGATGTCAATCGAGCGCTGGATCGGTACCGCAATGAAGTACGGCGAAGGCGGTGCTTTGCCTCTCCAGACCTTTGCTCACGGTGGTACTTCTCAATGGTCACACACCGCAAATTTCGGCAACTGGCATTGAAGCATCTTGATACTATCCTCCAGCCGTATATCAACGTCGAGCCGGCCGGGCAATCACTCGCCGCGGCTTTGGGTACAAGGCCTACGTACTGATTCACGCGTTACACGGATGACGCAACGCGTATTGTTGAAGCGCCGGAAGCCGGTTCGTTAGGCATCGGTACCTGTGCTGTTCCGTGGTCAAGTCGGGTACACGGTTGCAGGAATGACGCTGGGGACATTGTCGAATCGCGTGATGGATTGCGATGCGCATCCGGTGACGCTATCAACACTGGTGCGCGTAACAATTCGTCTTCGTTGGCATCGGGTTACAGTCTGGACTTTGGTCTGACGGGCGGCGTAGTGGCAACCGGCACCTTCTTCAGTTTATCCGGCCATGCCTTCGCCGCGCCTCCAGGTACCACTGGCACCGAAAAGCCGGAAAGCCAAACACTTCCTGTTGCAGGAAAGTGAACCGAAAAGTGGCGTGAATGGGAACTACGCTTCCCAAATAATGCCCTACTCCGGCGTGCCTGCGCCGGGCGTTTATCTTAAACTGCGCTGTTTTGCCAATGGTACATGCTCGTATGGCCCAACACACCGTTTATTTCCGGACGCCTACGACTTCAATGCCGCGAAGCGACCCTTCGTACTCTCATTTGATATTTTCTTGCGCCGCAATGGCTTGGTGCGCCGCAGCATTCGCGGTGTAGCGAAAATCTCCGTTGCTGATTTCCTGCAATTAACGCTCCTTATGGCTGGACGCTTACGCCAGCAATTCCGTGGTGAAGGTTTCTGGATTGAACGCGACCAATGAAGATACGTGCCATTCATTAGTACGCGAGCATTTAAGTGGCTGTTTATATTCAGGAAGCCAGTTCAATGTTGCCTGTTGCCTGCCGCATGTGTTTGCTTTGGCAGTATGCACCACAGCAGGTGATGGATGTCATGCCGCGCGCAGCTCAAAAGCAGCGCAAATTTCCGCGCGGATGATGAACGAAGGCAATCCTTGCCAATGAGTTTTCCGCCAGTCAGGTAAAAAGTGTTATGCCAATATCAGCCGCTGTGGTATGTGTGTTGCGCTCACACATTTGATGGCCGCGTGTTTGGTGCGAGAGAAAGCAGTGCCAAATATTCGATGCTGTTTGCTGGACGCTCCCTGCTCATGGCAGGCGTGGTGCGTAAAAATCCGGCCACTTCCATAAAAACTTAGTGCAAAGAAAGCAGAAATCAGGAAATCGCAGCTACACAGCAGGGCTTATCGACAGCGCCTCGCCATTACGTCTGGTGGTATGGTTTACTCGACCTGTACCTTAAACCCGGGGAAGAAAACGACGTTACCTGAAAGAGACTTACCGACGCAGTAGAGTTTTCACCAGCGATCTCTTCCACGGTGCAAACCGGCGCGCTGACCGAAGAAGGCTTTTGCATGTTTTCCCTAATTTACGACTGCGAAGGCTGTTCGTTGCTCGTCCGTAAAAACTCAGGCGATTCCCTTGCCCCGCCTTCTACGAGTCGAGGTAATTTCCGTTCTAGCCGGTGAATCGCAGCTGGGCCGGTCGTCGGCGGCTAGGTCTTGTGGCTTAAACTGGGATGAAAACCTGCACCTCTGGCAGCATGACAAGAACTGGTTGTTCCCGGTGGCATTAAGCCTGATCAGTAGATCCGATTTCTCGGTTGGGGTTCTTCGCTTTGAAGACGCACAACAAGGATTATCGCTGGCAGCGCAAGCAGTTATTACTCTTACCTCACCAGTAATATGAACCATTCGAGCTGGCCGCAGAAAGCGGAAAGTGGTATCACAGGCGCGATGTTTACCCTGCAAACGCGCCGGCCCGGATGATCTGTGGTTGCTTTTCCAGCATCAACCGGTGGTTTAGCAAACAGATTGGTTCCGCGATTGAAAAAGCAACAACTATCCGCGTGGTGGGTGCGCGATGAGGCTTTACTGACTGACGCCTGTTACTACGCGCACGGCTGGCACATTCGGCTGCCTCAGCAAGCTGAAAATGGTGCAATCGGACTGGTCGTACCACAATCGGCAGCTAAATGGAAACTTTGAGTAAAAACCAAGTGTGCGCATGAGGCGCTTTTGGCAATCGACGACGGCGAATTACGGTGAATCACCGGGTAATCGAACGTTAACCATTCGCCTTAAATCTGGCTTCGATTATAACATGCAGCGGATGCACCGGTGCAGAAACCAGTATCCCTACCCTGCCATCGCGAACACTCTGTCCTTACCGTACCCGTTACGATCAACGTCTGATGCACAGATTATACGTCTTGCACGATCCGCCCGACGTCGGCATGGCGGAGTTGTTGTCTGGTTATTCCCCGTTGCTGCATCTCTCCTAAACAACGGTGGCACCACTTCGGGATGAAATCTTTGAAAACAGTACTTTTGTTTGCTACACCAGATGGCGGTTGGCAAGAAAGATATTGTTGTGGATGTCTACACTTGAACAGCAGTGTCTTTATTCTATGAACGATCAGCAGTTCACCAGGGGCGGTTGTTTCCGGTGAGGATTTTATGGGCTGGCGACCTACAGGAAGTACGATTTTAATTGTGCAGTACACAAAAGTCAGTTCACTTTAAGACAGCACCGGTATCAGTAATACAGGTTGCCAATATCCACGCGATGTCGCAACGGTGTATGACCGACCAAAGCCAATCAGCACACCTGTAATTCCCTGCCTTTTGGCATTCACACCTAATCGCAAGCAGCTCCCACAAGACCTGTTCACAAATCAACGTCCTTTGCCATTCGCCATATCATCTGGATAATCGGCGCAAACATGCCTGCTTGCCAGTGCGACTGTCAATACTTCAAGATAAAAGGCCATCTGACATTTTCCAGCGCCGTTTCCTTGTTTCATTGATTATCTTATGCCAGCACCGTAAACCGGTCGCCGCCGTCATCAACCACAAGACATCTGGGATGCAGCGCATCCATCATAAGCATATCTGTTCATGATTGCCTCTTTACCGCTAAACCCAAAGTATGTTGTTCCAGTGGCGACAACGTAAACTTTGCGACCCCGATCAATAACGTCTCCCACTGAGATAAGTAAATCTCATACGGATCAAAACGTAATACCACCGCAGCGGTTCTTCTCGAACAACCGTGACATATCGCTTAAGAAAGCGAATGTCGCCGTGATGACCCGCAATTCTCTGATAAGCCAGGCGCAGGCGCTGTTCATCATCCGCACTAAGATCACATAATCTTAACAAGAATGTTAAAAACGCTGGACTCAGACGGTGCGGGGTGTGTGGTTATTCTCCGTCAGCGAAAGAAATGCGCTTCTGGCTTTTAACAGATAAAAAGACCGAACACGTTCTTGTTCGGTCGAAATATTCTTAGGAGAGAACTTCGTGTGCGCTAAAGTTGTAGCGATAGCATGTTGAAGCAGTTACCTTGCCCACTTCACAAATGACGACGCGAGGTTTTCCAGTTTGCGTGCAAAATAAGATTGTCGCGGTAGTGGTCATCAGCTGAAATGTTCATCGCCGTTCTGGTAAGAAGAACTGGGAGGCGGTTTTAATGTAATCAAAAGGCTATTTTAGGTAGTAACAGAGTTTTCAGCTCGTTCCTAAACGATTCCAGACTCATTTTCGCCAGGATTATTTAGGATCATCAATCTGAATCACCAAAATAGGTTTGGTATTAAGATGTCCCACTAGCAACTTCCTTTTGTGCGATATCGTTTAAAGAATACCACGGTACTCCGGATTAATACCTGCAAAAACATTACCGGTCGGCAAGTCTTCTCACTTCGCGTTAAGCGCCCATTTACTACCACTTCAAAACGACGACGGTAATCACCTACACGGTGCAACCAACGCCGCTAGAGCCTGGTAGTAACAAGAAACGCCAGAAATACTTTCATCATTTTCATCCATCCAAGGTTCGAAGTGTAAGCAGGCTGATGATCACCAGCACTACCCTTTCTCCTTATTCAGTTTGTCATCACCGCCGGGGTGCCGCACGATCTTCATCCTACTCGCGCGGTAAAGAAACATAACGATTAGCCAGCGCAGCCCTGTCCTCCACGGAGATGGCTTTGAAACATGCAGAAGTTGTTAAAGTCGCTCGTAAGCGTAGGGAAATCCGGTAATCAACAATGCATTCACTTTTACGCTTGCCAGTACGCCGATCACCGCAAAATGCCCGCACACCCGAGGAAAACATCAGCGCCTGGTGCTTTGGTGTCGCCAACGGCCTTTGATGATTACCACAAACACCGGCAGTAATCCCCAAACCGCCGCCGCACAAATCGGTGAATCGCGTGATTAGTCAATCGTTTCTTTACCTTCATTCAGCGTCGCATACCTCCCTTGGCAAGTCGTGCGCGGTAGGTAAGCATAAGCAACAAACGTGGCATATTCCGCGTTTACGCAGAGCGACGATCAGCAGTACGAGGAGGCGGCGAGAACGGTACCATAACCGATGCCGCAAACTGCGTTTGCAAAACCGCCTGTTTGCATACATCTGTCCATCCGATTCCCATCAGCCACCCTGAACGGCGAGCATTGCAGTGCTGATCAAACTCAGGCAACGGCGATACTGTTGTAAACGCAGAAGAACAACTACCGCCAGCAAGCAGCAAATCGTCAAAGACTGCCGAGCACACCGGCTACGTACGGCCTGGCCAGCATCAGCGAGGTGTGTCGTAGATAAATCATAGCACGATCGGGTAACATAACGCAATTCCCGCTAAAGGTGTAGTCCTTTCGTTTGCACCCGTCCCCAAACAACGCCAGTCAACGGTGTAAGTTCCGGGTTTCAACGGAATCAGCCAGTGGAACAATCAGTTGCTCCTACTCGGCTACTTCGCCGGCTATCTACCTGTCTTTCGTTTTGGCCCAGCGTGATTTTACTACTAGAATCCTGTTTCCGCACCTTCAGTTTAAAGTAATTCACGGTACGCTGTCTACGCGTTCCTAGGATACTGATACATTCCATCACGCATGTACTTGGGCTGAAGATGTCCTGCAAGTGGTCAAATTCTGCTTGCGTAGCGAAAAGAACGCGTCAGACGAACATATTATCTATTCCTTTGTAACCACTTTTACAAAACCTTGTGTCTGTCTGGTCAGATCATCAATTCCGCTTGCCATCGGCTTTCCTCTTAATAACTTTACCGCGAATAATGAAATTAGAAATACGAAAAATCTGGCAGCTTCGCTGGATCAAGCAATGGATAAAAGTGAATGTCAGGGGTGAAAAACATGGGGTGGCATTAAGAACGCTACAACCAAGTGACGCTGCGGCAGTTGAACGTGAACAGCCTACGAACTTTGCGCAGCTGGTTTCGCGAGCGGCGCCTTGCCCACCGTTTAGCTTCAGGTCCAGTATCTGTCACGTTACATACGAGCCCAAACTTTCCATCCAGAACTTATACAAGTTACTGCCCGCAACGCCTGCTAAATTATAGTATTTTCTAAACCGCTCATAATTGCGGTCATTAAAAAGTGTTATCGTTCTGGAAAGTTTGCACTTAGCGCAATATGAGCCTCGTAAAACCTCTCGAACAGGTAGCTCATCATCTGAGTTTGGCGAGGGCCTGCCGACATAAATATCGCTGTTAATTTTCCATCGCTTTCTTCTGGGGTGTGATTATTCGCGACGTACGCCCTGCCCTGATCTCCTGTTGAGCCCTTTGTTATGCCGCAACGACACGGCGAAATGACCATCCCGTACCGGCCTTCCCGTTAGATAACAATCGCTTTATTCATTGGGGCTGCGGTGTTTCACACCGTAGCGCTTACAGGATCTACATCCGGTCATGGTGCATGTCTACGACCGTCGTTCCAAGACTATCACGGTGTCGATGAACAACCGCAAAGTATGGATAGACCCGACAACCTGTTCACACTGTTTACTACAAGGCAGCAATATCTGGGAAACCCGACCTGCTGGCGTCGCCGTCGCCCTGTAATTTTTCCTCAATCTCGGTGCCGTGCTGATGGCAAATGCCGTGTGCTGGTGCACTATGGAATGTGGTCGTCTCATCGTTTCCGCGCCGTCGTAGTTCGTATTGTTAGTCGGTCGCTTGTTCCTCACAAGGTTGCCGAGCGATATCATTCCATTACGCTTCAGGCTTTTTCGGCACGGAGCATGCCATATTCGCACGACCATCGACCGATACAAAACCTACGGCGGTTTACGAGATCGTTGAGATTACCTCTGTTGATGTCATTGTTGACAGAAATCGTCGCCGCCCTGCAAACCACAGTGCGCCCGATCGTCGTAGTGCTAAGCGATGGCGATTCATGTCGCATCACCAGCTCATAGTCGCCGGCTCAGCCGTGGATTGAAGATGCCAATCCCACCTATACGGCGTGAATGGTATGTCGCACCTGCTGCTGCTTTGACCTGCGCGTACTACCTAGAATGCCCGGTAGTGGATTGCACCATAAACTGGCCGTCGTTGTGGCACAGGATCAAACTTCTGTAGCTCGCCAGCGTGCTCTCAAAACGCAAGCTCAATGTACGAACGCCGCCGGGCTACATCATCACCACGCGTTGTGACTTCTATCACCACCGCATTGCTTATCGATATTAAACACCTCCGGCTGGACGGCAGAACAGATAGCCGATATCTGGGCGTCCGTCATTGGTAGCGAAAGCCTTTCACCTTTGGCAAATACCGTGGCCATGGTTTCCGACTTACGTTACCCGAACACGATCCAGGCTTCATCCGCTGGTTGTTTATGCTGGACATGGGCTACGTTCTACTGGCCTGTCCCCAAATACCAGGTCCGTAGCAGTATGTTCCTACTTAACGCGACAAAAACATATTCCATCGCCTTCGTACATTCGCGACAAATTTACCGCCATACTTCGTCCATGTCGGTACAAGTATAAAAGTATAATTCATCGGTTTCAGCTCGCGCAATTTAGCGACCCATTTGCCCGGTTTCTATGTTGCACACAATCGTACAAGCCGGTCGTTACAATAAATGCGGATAGAGCCTGTGCGGTGACGTTGTCCGCACAGGCTGTAACACTATGTACTCGTAATATTGCGGATCTGCAGGTTACCCTCTTCAAACTCACCAGTGGTAGGAATTGGATTCATCAACATCATTATTTACAACATCAGCAAACGGTACACAGGCGTCACGCCGTAGAATCTTCCGGGCGTTGATTAATTGCAACGCCCATCAACACCCCACTCCCGCCGCATCACCTGCTCAGCGAAGAGCCGCAACCCAGTTTATAATACATCTATGAGCATCAGATAATCATTAAGCATTTTCTTCTTCAGAAGTACCGTCTTCGTACCTTGTTGCCCAGCTCACCACCGCAGCATAGACCAATATGGCGTAAACAAAAGCCGATCTATAGCTCAAGCGGCTAAAACTGAAAATCTGGCATCAATACGCGCCATGAAACCATAGCCATACACCAGCAACAGGTTGTGTCCTTGCGAAAATGTTTGCGATAGTGACAACAGAAACCAGAACTTCAACGCCATCACGGGCGACTATCTAGTGTTCACTACGGTAAATTCACCACCTGCTTGAGAACTTCCGTTTGTTTTAATACGACGCTCCACCGGTATCCATATCCAGTTCAACAAAGTGTCTGGGTGTAGTCATGGAAGAACTCGCCCTGTAACGCAATCGCGGTTTCAGGTTCTACAGATTGGCAAGCAATCCAGGTCCTCGACGGATCATCAAAGCAATACAGCCGTGGCTTCCAGGTCTTGCAGTTAATTGCTTCTTCGTTGTAAACCGCGCTGGCGCTCCCAACCCACCAACCAGTCGGTAAGCAGCATAGCCTTCCAGCATGATGTTTCGCGTGGCGGGTAACTCTTCCTGTTGCTCATCACGCATACAGGTACGGTATAAGCCAAGATTTTACCATGGCAGTTTGAACGCAGGCCAAAACGATGCTGGTAATCAAAGGCTGACTTCGTGATCTTTGCGGCGCGGCAAAAACAAACGGCTCGGCATCGGCCATTCACGTCCAGCAAGGCGAACACTTCACTGGTGGTGGCGCTGGCCGTAAGACCTTCCTGGTGCTTCCTGGTCGTTTTATGCAGGCGACGTAATAGGTATCGTCTCTTTTCTTCGTGAATCTGGTTATCTTGCACGATGCTGGCGTACCGATGGCGACGCACCAGACCTGATGAGCAGCAGC
>40ec00e1-8838-42fe-9f6c-01c29065fccf_Basecall_Alignment_template nanopore2_20160729_FNFAB24462_MN17024_sequencing_run_E_coli_K12_1D_R9_SpotOn_2_26075_ch359_read469_strand pass/nanopore2_20160729_FNFAB24462_MN17024_sequencing_run_E_coli_K12_1D_R9_SpotOn_2_26075_ch359_read469_strand.fast5
CTTAGCTACGTTCAGTTACGTAACGCTGTTGTTTCGCATTTATCGTGACTTTCGCGTTTTCGTGCGCCGCTACAGCCATCCTCAACCGTTGCCTTTAAGGTACTTAAATCAGTGTTGGTGGCGGCGATAGTCGATGGATCTAACTGTCAAGCTAGCAACATATATGGGCGGTGCTTGGGTTGCCGGTGACTTTCACGGTTGTCTGTGTGTCTGTATTGTTACGCCTTGGGTGTGGAAGATGCGATCACCGGCCTTGTGTACGCCGACTTTATTGCTGGTCAAAACGAGCTAGAGCCTGACCTGGAAAAGTTAGTTCTCGCACCCGCCCGCCGCATCGCCCCTTCTGGCGTTACGCTAAAGTTGATGACCTGACCCTCACTGGTACCATTTGCAAGGGGTTAGCGTTGCCGTCAAGTAGCGCCTGTAGGGGGCATAGACACCGATAAGCGGACTAAGACGCCGTGAGTGTCAGTTTTCATCAATAGCCTCAGTTGTTTGAAGTGAGGCTCATTCGGCGGGGATGCTTTCTTCGCCCATACGAAACCATTTCTTTCCAGGCGTCATAAGGTGACCTCAACTACCACCCTGCGTAATGCGTAGAACCGTATTCTGGCTGATGATGATCATTTGCGAGATGGCTCTGCACTGAATATCACAGGTTGATGCGCAACCAGGTTTACCAAACTGGTCGTTAACGTAGGCTTTGCTGCCGTCTTGTGCGACCGTTACCTGACCTTCCGGTGTCTCCAGACTGGTATCGTCGTTAACATCTGCATGGCATTTCAATGAAATCGCGAGATGACTGGCTGAGTTTATCTGCCGAGGCTGAGCTTTATTTCAGTCCGGCGACCTCCAGTACTTGTCACAAAATTTCAGCAAACCGATCATCCGTTTCAACTGGTGCTGCTTAAGCGTGACAGAGTTCCTGAAGTGCTATGCCTTCTACCAGGTTGCCGTTAGCGTCAGTGACGCTTACCGTCATGGTTACGCCTCAGTCGTGCCTTGACAAATAGTGCTCTGAAGGTTAAGGAGGCTAGTTTGCGGTATAGCATCGGCAATCAAAGTCCACCTGTTCGTATCACTGACACCATAATTGTTCCTTCTTCTCCACGGGGTAGGTGCCGGATTTTGTACCGCTCAGTGTAACTTCAGCCTTACCGTTGATATCAATGTGGCAGAACCACCTTGTCCGAGAAGTAAAAACTTGCGCTCATCTGCCAGTAGCGTGGAATGTCACCGCCTCATTGCTAACGGGTTGCCGCCGTTATCAGTCACTGTTGCCTGCCAGCTGGTCATCCAGCGTTATTAGCGATAGGTGTCCTCGAAGTAGCGATGCGGGTGCCTGCGCGGTGAGCGTATCCTGTGAAGTTCACCACCAGCTACTCCACTCTTACCGCCAGTCATCGATGCTGTAACAGTATGAGCGCCTGCTTTTGTACCCTGACGTGACTTTCTTTGCCTTCAGCATGTTGATCGCTTTACCGCCATCGCTCAGCGTGAGTTCGCCTTCACATCTTCCGGCGGAAATGTTACGCACTCAGTGTTGGCTATCGTGCCCTCTGTATCAGCGACTGTATTGCTGTGTGGCTGGGTATTGTGTGAGATCGTTGTTGTCAGCAATCCTGCGCAGATCGCCAAAGGCTACTGCTTGTATGATTTCAGCATTCGCGACGTTCAAGCACGCAAGTCACTGTTTGTTGCATCGAATCGCCATTTCGAGGGTTGCCGTCGGTGTCAGCCCGGCTTTGTAGCGGTAAAGCTTGCGTAAAAGTGCCGTCAATGGTTAGTATATAGCGTTATTACTGGGGTCCACGCCTTCACTTGGTGAAACGCTGGGGTTACTCCTGCTGGGAGACTACGTTACCGTAATTATCCTTCACCTCAATATACAGACGGTTGTCTCGCCTGCGGAAGTTGTATCAAAGATGCCAGCAGCAGGTGAGATGTGCCGTAGACGCATCGGCGTTGACGATGGTGATGTGCTAGGCGTGGGGCCACCATTTTTCCAGACTGGCCTCAACGGTATCCGGTCTCGCTCCTGATTCTGAGGCAGGTATTGTATAAGTGACAGTAGCCTTACCCTGTTCGTTTCGTCACGGCTTGACCGCCGTTCGTCCATTCGGCTGTCGCTGCGTTGCTGGTGAGTTCACGGTCACGCTTTCGCGGAAAGCCATTGTATCAACGACTGACGTTGGTAGTAGCGCTGCCAGAGCTTCTGCAGAGTACCGGCGATTATGCTGCATGTCTGGGACGAGCATAACTCGATAAATTTTGCCGCCGCTGTATGTCCGTCACCTGGATTTGTTGTCCTTGGCACCGGTATTACTTGAGTGATGCAGTAACCGTCTTCTCACCAAAGAGCCTTGCGCCTGCGGTGGCCTGCGCGATGCTGTGCGAACTCGTTGGTGACCACCTCCAGGGTCAGGGTGGGTCCTGAAGAGGCTGAGCTGAGATATTTTCCGGAAGATTATTCACCTCATTGTCAGACGATCTTTTAACCGTTGCAGTTAGCGTTGCGCTATCGACGCCATTACCTGTGATCTCATCTTTGATATCTGCAGGACAACCCTGAGCCAGGCTTTTGTCCGCCACAAATGTTACCGGCTGCGAATGCTGCTGGTATTGTTGTACCCAGCGTTGCGGTGACGTATACGTCGCCCGCTTTTTACCTTTCAACGTGACGCCGCTTCCCATTAGCCTGGTAGTGGCGTACCGTTATTTTCAAGTAAGTTGCACGCAACGTCCTGTAGCATGGTAAAGTTACCATTATCCCCTCTGGATGATTCGACGATCTTTCCTGTTGCTGTCAAGAGTTGTCTCATCCACGCCATTCCCAAGCAGTTTCCGCTCGATGTTTACCGAAGCGACAACCGCTCTGTCTTTATCCGCCACTACGTCATTGGCTGGCCACATCGCGGCATTGCTGTTAGCCAGACGAGCCATGATCATATGCGTACCGCTAACGTGCCGGTCAGGAAGCGGTGCAACCGTTACTATCCGTCTTCTTTCCTCCGTTGCTAATCGAGAACTTCACCCACGTGTCGTTTGGCTGAAGGTGATTCACTATCACGGTGGGTTACCATTTTATCCTGCAAGGTTGCGGTAGTCGCTGTGCCTTGGGCTAATGTTGTTAGTATTGGTGATATCACCTGAAGGCACACTGAGGGTCAGAACGGCAATGCACGATCACCGATAAAATTCACCTGTTGATTAGCACAGGAACCAGAGCTCACAAAGCCGCCCTGTCACTATTTTCAAACTGGTCCAGCATGCTGTGGCGATCCCCGTCGTGACTGTCCACTTCAGTTTGGCTCAGTTTCGCCTCTACTGGAGTGCTGTTAAGAAAGTGACCATGACGTCATTGAGCAGGTTGCCCCGCTCCCGGACGGTCCGCGGTCATTTGACGACTGTCATTGCCGTCAGCAACCACTTCATTTTCGACTTCTGCAGATCAACCTGCGGTACTCGAGTCGCCGACAAGGCGACGATTGGCATTTGTTTCACGCCGTCGGGTGACTTCAGCGATGTTGTCTTCCTGCTTACTGCGCTTTTCAGATCAAAGTCGCCCGGACCGTGCATCCGTTTTGCGGTGTTTTGATTGTTAGAAGAAGTTGCCGATCCATAATACCGCAAACGACGGTATGATCATTGAGTGGGTTGCTTCCTTCCATCAGCGGCTGATGAACCAAGACAGTGTTTGCTGCATTCTCATTGGCAAACACCATTGTTGCTGGCGAATAATGTCGCAATTTCGCTGACTGCGGGTTGGCGTGTTAATCAGCGAGTATACAAAATCTTCCGGTCCAGTTTGCATTATGCTTCGCAGTAGACCCGCACCTGCCTGCCTTTGGTATGAGCGGTATAGGTCGCCTTATAGACGCCATCTGCGGTTTCTTTTCCAGTCTGGTGACTCGGTTTCGCATTCAGTGCGGCTGCCGTTATTCAGTTGCTGTTTTGTTCATAACGGGTTTGTGTTTCATCTCAGTTCTACCGTCACCTCTGTTAGGTTGCCGGAGATAACGGTCATATCAATCTGGTGGCCATTAGGTTCAGGATGACGAGCAGAAATGATATTCACCACGGCAGGGGCTTTAGCCGCATCCACCGGTCAGCTGGCATCTTGTCAACGTGCGAACATCGCTCCTGTGGTGGGATCTGGGTATGGCTTCCGTCACCATTATCTTTCCAGTCAAAGGGTGATGTCCTGAACACCTTCGTGACGCGTCAAGGGCATAGCCCGACATGGGATTACCTGCTGCATCATGCTGCGAAAAGTCGGTGTGGCGGTTGAATGGGAATCCGCGTTCAATATTTAGGTACCAACGTGCCGAGGAATCTTTCTACAACTTAGCGTAGAGTGCCTATGGAACGACCACCATGCTCTACGATTCCGGCTCCGGTGGCGACATCTTCGGCGGTGACTTCAATCAACCCGAAGTGTTATCAGTTTCCTGGCGTACTGGTAGACGGTAAGCCGGCAGGGTAACCAAATATCTTTACCCGTTGTAGTACTTTGCCACCAACGGCTTCCAGTGCGGTGGCTTCGACGTCTATAACCTTTCAGGGCATGTTGGTTTACGGCAACGACGAAACCGGTGATTTCACTTCCTGACTTCCCTGTCACGGGAATGCGTCGAGTCCAGCGGGCAGGCGAACCAGTTCTTGCGATATTCAGAACGATATTGTTGCTTTGCGATCCACTGAATCATAACGGCTGCCTGCAAGGCTCGCCGTGCGGCGACTTCATTCCGGGTCAAGCTGTTTCTGCATTGCCTGCAGTTGCCGAGGTAAATCGACGGCAAAACGAGGTGTCATTTTCGCCCTGTTTACCGGCGTTGCTCCCGCTGAAGGTCATCAGCGGGAAGGGTATGGTCAAGTCCGGCAGTTGGCATGAGGGATTGCGCCGTCGTCTGTATCGAACAGGGCCACTTCATCCCTTATAATACTGTTCATCAAACCAGTTTACCGCCGAGTGCGGCCGAGGCGGTATGCCGGCTTTCTGCGCGTACATCCCAGCCACATTGGCCGGGCGTGCTCATAATCGTTGTCCAGTTCAGGTGCGCTGCGCCAGTTGGTCAATCCTGTCTATAGCCGTTACTACTTAGTACAGATAGTCGCGCCGGTACTCCGCGCCAATGCCGGCGCGGGAGTATGCTGGCTAAGATCGTAGTCAGAAAAAGTTGTTGCCCGGCATCCATGTAGAGTGAAATGACGCCAGCCTAAGCCGTTAATCTGCGTACGCTCGTCGGTACGATGGAAGTGACATGCTGACGAAAAGATTATCGGGCGTTTCGCCACCGCAGATGAAAAATCGAACTGGGAGTTCTTCAGGCCAAAATCTTCATCCACGCCCAGCGTAATTCTTGCAGTACCAAGCTTGGCCGCCAGTCATCTCTTGCGCCTGAAGCGCGAGAGGCCACGCGCCGCCTTGCGCTTGCGCTCGCTGTTCTGTCTTCGGCGAGCAAGACCCGATTTGCTGTGAAAGTACTGACATCTGTTGCTCGAGTTGTCCACTGCTATTACCCGGCGGCGGGGTTAATTTTTCACCACTAACTTGTACGGGACATCAGTTCATCACCGGCGGACGACCTCAAAACCTCCGAACAAACGTACGAAACTGGTTGAGTTGCATGCTCAACCACCAAATACCAAAACGTTCAACACTTTGGGCCGGTGCTCAAGGGTGCAAGGCACCGTAGTGGCATTTGCAACGTTTGTTGAGAACTGGTTGTTGGGTTGCGGCGATTTACCACCTTGTGCTGCCTGTAGCCACCGAGAACCTAAGTTAGGTTATCAGACAGATACCGCAGTTAGCAGCATGGGTTTTAATTCCCATCACCATAATATTTATCGGTCATTTCTTCTTCTCCGCGCTTCTCTTCTTCGTAGCCGTACTTTACAACTTCCTGAACTGCGCAAATGCGCCCTTTCTGCTTTTGTGAAAATGCCATCCCAATATATGATTGAAAATTATTAACTTTTCGTTAGGCAGTTTGGGTGTGAGTTGCAAGAGGAGACTACTGGAGTAACTCTTGGGATTTTATAATCGAGGGAAAATGGTGATGGCGTTCGCCTTAAAGCATACTCAGCCATAAGGTCGGGCGGCAAGATGTTGAAACCGCGTTAAAAACAATGTGCCAACTAAGGTCCGGTATTTGCGCTAAAAGCTGAATTTTAGGTGGCTCCTCAGCTGGACTCGAACCAGTGACGCCGGATTAACGTCCGCCGTTCTACCGACTGAACTGGGAATCGTGTGAACAGGGCCGTCTTCTGCTTGGTACCTTGTCTGTCTTTCGTTCTCGTCCATTTCAATTGGTTAATTAATCTGCAAAGTTGTTGGTAATGAACATTCGTCGCGAAAACGAGTCTGTATCATTAGCGTGATGCAGTCTCTGAGGACTCTTGTTGATAAAATTGGCGAAACGTTACTATGAGAAACGAAGACAAAAGTTCTGGGCGCTAAAAATATTCAGAAAAGTACAGCAAAAACATTCCAGCAGGATCGCTGGCTGCATAAGCATCAATATGCCGCATTCTCGCATAGCCAATTCGTTTCTTCCTGAATATTTGTTTCCATTTACAACTTATGAAGAATCAATGTTTTCAACAACCTCACGGAATAAAGGGAACTCCGCTGACTTGCGGAAATCATAAGGTACAGGTGTCCAACATGAGCGACTTCATGAATAATCAGGTTAAACAAAGCTTGTCAAAGAATCCCATATCAACCAGTTCAAAACGATAGGCCTTGCCAGCTCTGACCTGACTGAACAATACGTTGGTTATGCATGACCGACTCCTCGTCTTCCATTCATCATCGACCTAAATGCGCAGATAAATTAAGACTTCATGAAAACCATCTACATTTCGGTCTAACTTTCAGAACGAATTTGAGCAAAATGAAGTACTTTATCCGGCAGCTTCTTAATGAATCGGTTCAAGCCCTGTAAAGGAACAACCACTTTGCTGTAAAACGTTCGGCAAGAGTGACTAATTTGCTGTTCTGTTCCGTCGAACACACCGCACGTTAAAGGATCGATATGGTGCTTCCTGCCGAGGAAGGGCGGTTGATGTGCTGATTCTTATACTTTCGAGAACCCATGTCATCGTTTTGCTCGCAAACTCGTCGCGAACAAAATTACGGACGGGGACTGTTAAAATACCAAGTATTCACATCTGGCAACCATCTGAACAGAGATACCAGGCAGCGGCTGAACAGACCGGTCTCGAAAACCGGGTAGAACGCTCTACAGAGTTTCAAATCCCTCTCTCCACCACTTTATCAATGACATCTCCGGCTTCCCGCCTTGCTTTTCCTAAACAGAACAATCCTTAGAATATTCTTGGTTAGATAAATGCTGTTTCTGTTCGATACAGCATTCAGCACTTGATTCGCTATGGATCGACGAAACTTTCAGGCGAAAATATTGCAGTTATTCAGTCGTTTTCTTATCGCTCACCATTATTCTTTTAGACATTCATCCTATGAAACTGCCGCAAAGTTAATTGAGCAGAACTGAAGTTGTGAAGAAGGGTTCATGGTGAGTCAAAAGACATGACCGTCAGATTAAAGCCAGGACAAAGTCCATGGTATTTCAAGAGTTGTTGAATTCAGCTTTTGAAAACTTACTGTATCATACTAACAAGTAAGGTTTAAATAAAAATTAACCTGTATTTTGATAAATCTACCATTCTTACAGTTACAGATTTCTACTCCTCCTTGTTGATAGTGAAGAATTGTTGTACACCGTAAACAATTTACAACGTTGATGTCCATAGTTCCACATTTCCTTATGAGATCGACTTATTTACAGCGAGGCATCATTCCTTAACAAGTATTATCTTTCTGAATGTGGTATTCGAAAAGTGCTGCACTTTCAGCGTGAGCTGCGATTAAAAGTAGCCTATTGCGAGTTTCGTAGATATTTTATCAATTACTTTAATTTCGCTGTTTGGAGGTATAAAGAACGTGAAACAAAAGAAACTCCACGATTTTCCACTGTAGCCATCAAAACAATCAACAGGAAGTGCGCAGGAAGGTTATATAAAGCATGATGTGCGTGGCAAGCCGCTTTTGTTACCCGAACAGGTGGCGGTGGCACAATGGAAGGATCATAACGGTGTTTGTAATCGGCGTGAAAACGTAACACAAACGAATATACCCGCATTGTAATGTGTTTCTCGCATCAGATAAATTTCTACCTTCAGAAACCAACCACGGGTTCATCGCAGCGCAAGTTGTACAACAAAAAGCAACGTTATCTAATGTAAATAATTTGAGTTTTGAGAATGGTTCATTTTGCTAGCTCCTGTGATTTTCACGGTCAAGCTATCCGAACAGCAAAATTCCTTATACGGATGTGTGGTTTAATTTGTTATTTAAAATTGATAAGTGCATATTGCTTCTTGACCAATATAAACAATGGCGTGAGCACAAGTATCTCTCTCTCTATTGGCCGTATTGTATGGGATCCGTTATTGGTTAACTCAATGCGGGTTGGCTTATTAATATACAGACACGTCGTGATGAGCGTGTCTGTAGCCTTTAGATTCATTGGCGTTTGTGGATGGACCAATTGGCGGTTATGATAACTTAAGCGGCATCACGAGGCGTTATCATGAGAATATAATGGACATCATTTCCTCGACCGCTTCTTCGCTACTCAACTGATATGGATAATACGTTGGCCAGTTTTCCATTTCATTTAATAAAGATTACCAACTGAATCACATTACCCATAAAATGTGAAAATGAGATGTTTTCATTGGTGCAATTATATGATCGCTAAATTGACATGTATTTGGGGAGAACTGCTTCAAGGATCTTTACATTCGAATAAGTGAACGCTTCTTTCTTGCCTACAGTTTATGGTGAGTATTTTGTATCCATCGTGATCATGCTGTATTTTACGATTGTTTCATTATTCCTATGGAATTCTTAACAATGCCGTCCCTCAATGCCAAAATCATCTCGATATCTGTTGCTTAACCTTTTGTGATAATAATCACTAATTTTCAGCTAAATGTTTGGTTTGTCACCGTCGCTTTCTTCTGAAGACAGGGTCCAAGTTGCCACTTTGCAGTAAAGGATAAACGGATTACCAGACTCCATCGGTCACTGAGCGTTCGGTTTGTACATTTGGCATCGTAAAACACCATTGTAGCTTTTGATTTCGACCTCCTGTTAAAAGGGTTTGCCAAGTGACGGTGATGATGACCACAAGAAAAGGCGGGGCGCTAACAATAGACACCTAAAGCAGCAGCCGGTTTATGGCAAGACAGATGTAAGGCAGTTTCGCCAGGTTAATGTATGATGTGGCAATGTTATATTGTAACATATAGCAAAATGCAACAACTCTTAAGGAAACGAGAACATAACTTCTCGGTCCTATTATCTATCAACTGATAAATAAATTATTTGGTGATTTGGGGTTGGTAATAAACGAAACATAACCTAGTGCGATCTTATTATTATGCCGGATAGGGCGCTCGCGCCACATCAACAGGGATTTCTGTGCTGTCAACAATATGAGTTCTAGATAATTTGTTGTAGACCTACTTGCGCAACGGTTCAAAGAGACATAGCTTCTTATATGCAAATAAGGCTAAAAGCAGTGCAACCAGCCCAGCGTAGATGGGCGGCTGCGGTGATAATCTTACGGACTGAATAATGTATATTGGGGCAAGTCGACAAGATAGACAGAATTATACCTTTGTTGCTGGTGCTTTGAGTTTTCATGCATCCTTTTGGGTTGAAGTGAACTAAAGCAAGCAAAAATTACCAGCTGATATTCACTTTAAATGGGCCGGTGGTAACTTCCTTTACCTAACATGGGTGTTCGCTTGGCTCATAATGCGTAACGGTAAATACAGTGTCGCGGGCAAAAGCACCTAAAGTGTCATAGGCGGCGAGGTGCGTATCAATAACGGCTGTTTGCGTAGCGTGCAGAGGACGGTAACAGGGTCGCCATGCGAAATTTCGAGATTGCAGTGCGACCAAGGTAAGATGCTGAATATCTTTCGCGGATCGGCGCGGTCCGCGGTTGATCCTTGAATGACCGGAGAGCGGCCTTCGTCCGAGCGAGATGCGGGCGACTTTCGGCCATGTGCCTGTTTGCTGTGGACGCGGTAGAAATTCTCCGCAAATCCGGTACGATACAGCAGTACCCACTGAGCAGCATATGATAAAAGCAATACTTGTTAAGCTGGCACTATTTTATCGGATACCGCGAACAATAAATCATTCGGTAGCCTGCGAAGCCAAGCGGGTGATGCTCTAGATGCTGTTAAGCGTAAAACGCCGTATTCGTCAGGCGCTACCAGGTATTCCAGGATGGTGGCAGACGCTCGCAAGTCAACTCTTCACCAATATCGAGATTTAATCCACTGAAAGCCATATTTCCAGCACAATCAGTCACACCAGCACTACCATTCTCGCGTGCCTGCCAACCTGATCATCGTGTGAGCAGATACATTACTTCATCAGAACCTGTCACCGACCTGGATCTTCAACCCACCGCCGATAAAGCGGTCCTACTGGCAGCATCTGTTCAGTGCGCAAGGTATTTCGAAAGCGGCCTTACTTCTGCCTGCATTGCTGGTAGGTTCAGCCGCCTGCTTAATTGTACAGCGAAGCAATCCAGCTACCATCGACCACGCGCAGCATACGATAAATACGCGCTCTTCAGCAGGGAGGCACGACGGTTAAGTCGGCCGCTTGATCGGGGTCAATGGTTTGCCGCTTCGCCGCTGATTTCAGTGTCCGTGGATCCAGTTTCAGAGCTACCAGCGTGCTTGGCAGGATCAGCTTTATCCAGCCAGGTCGCGAAGTTATTATGGCCGGAGCTTTGTCTGCTGGCGTCGTGGCGGGTTGTTTTGCCGAGGCGGCGGGCTTGCCAACGAACTCCAGCGCTTTCACGGGGGCGGGCGGGCGATCGTTCCCTTCGCCAGCTAGCGGATCGCGCCTTGCGCAGCGTTGGGGGCCGCGAAAGGGTGCTGGTTGCACTGATGCCCAGTGCTTTAACACCGACGCTGCAAGAATACCGACTCAGCCATGACATCTGATTCTTTTAAGGGTGATTCTTTTTCGCAAGCCATGCACTTTTGTCCGTTGTGGCAAGAGCCGTTTACTGTTGGTCTGTCCAGGGGTGTGCACTCCCTGGTATGAGATCACTTTTATATTTATGCAGTACTGCCACGATAGGTTGAATACCCATATTGGCTAAGTAATAAAGACACATAGTAATGCTCGTTCACTTTATTAATATGAAATTCAGGATCTCAGGAAGAGAGAAACTTGAAAGTTTTGACGGAAATGGTCACCGGTTTCGTACGACGGTAATCGCCCGTAGTTACGGTTTACTCCGGAGCCTGATGCAATAATTCGTCCGGCATCCTTATCTGTTTGGCGGTATTAGGATTTGGCAACCTTCGTCGCCTTTAGCTTTTCAAGAAGTGACTGTCACGTCGGCGGCGGGTTTCCTGTTTGCTGGTTCAAAATAATGCACGCTAGAATGTTTTGTTGTGCGGCGCTAACCGAAGGTAGTAAGAAATGCTGCCGTTGCTGCCGGGAAGTACTAAATAACGCTTTAGCATGTTTATATCATGTCATGTGAATGAGTTTGAGATACTTGAAAAAGCCGGTAACCTGGCAGCATTACAATTTGTAAATGAACCGAGCTGTTTCTGCTGCTCGAGATTTATAGCATATTATTTTCGCGAAGATTCTACTTGTGAGATAATCAAGGACCCGGGAATGGGTAGCAGGGGCTTTCGAAGCGGGTTATGTCATCGATGCCGTTTCGGTGGCAGAGATGGGCTTTATCTTTACGCTGAAGGGTAATTATTCGTGATCATTCTGGTTATTATATGCTTCCGGGTATGGATGGCGGATCTTTACAAACATTAAGAACAGCAAGCAAGCCCACTGTTATTTGCTAACACAAGGAGTTCTGTCGATGACAGAGTCAGGGGCTGGACAGTGGGGCAAATGATTATCTAAGTAAAACCTTTTCATTTCTGGGGGTTGGCAAGGGTTCGGGCACGGTAAGGCAACATCACGCACAATTCAACATTAGAAATCGGCGGCGGCAGAATGGACTTCTGTTGGTCTGCGCGGGTATGTAGGCAGGGACAATATCGGTGTATTACACTGACGCAAGGGTTTCAGTTACTTTGGCTGCTGGCCTCCAGAGCTGGCGAGTATACCAGAACAGTTGCCGAGGTGGGGTGGGAATCGGCACGGTGACAGTACCAAATGCGGTGGACGTCGCCATTCGCAGGCTCCGCACACCAAAGATTGATAATCCTTTTCCTGAAAACTAGTACCTGATCCAGAGGATGGAGCTATTCATTCGTAGCGGTAAAAATATTGAAAAGGCTATCTATAGCCGTCCGTTTAACCTGCTTTTATTGCTACTGTCTTCTTTGCTGGCGCCGAATTGTCTGGACTCTCTACTAATGGCTTTTGTGAAGTGGTTGAAATGGCGCGATGATACAACCTCATTAACCCGGACAGCGCAGATCAAGCGGTTGTTGGTGGTAGGGTAAATCAGATACGTTACCTGTGTACTTTAACCGGATGATGGATGTTAGTCAGGATATCTTGATTATTCACTTGGGTATTAGCATCAATAAAATTGACAACCGGACAAATGTCGAAGTGATGGCATGTTAAATACTACCTGCTAGTGAGACAATCAGCGCAGCTGGCATTTACAGAAGCGTGTAGTACGAGATAGATGCTTTACAAGGTGTAATGTGATAAGTTTCGCCTCATTTAACGGTTTACTGTGGCTAAATTGGCTTTGTAGACCTGCTATACTTGAACAGTATAAAGTGTAACATTATAATTTGCATTGTCGCCATTGTACTTTGCTCCAGTATTAAGTCCGCTGTTAATCAGAACAGGATTACAGGATAAAAGTTGAGTGGTGGGCGCTGAATTATAGCGATAGCCGAGGCCTGTTGGGGTTAGCGCGTACCGAGAGAACTAAAACCTCTTGGGCGGGCGTTTGAATAAATGCATCATGCTTTAGTCAAAGATTTTGAGCGTCTAAGTCAGTTTGCTGACGATCGCTCATGAACTTAAGTATAATTAATGCATTACTGGGTCAGATCAGGTTACGCTCAGTCAAATAAGTAACTGGAATATCAAAAACTGGTGCGGAAACATTGGAAGAGAGCTGGAAGGCTACGCGGTTATAGAGAACATGCTGTTTCTTGCAGGGCAGATAAAAACAATGTTTGGTGAAACGGACTCACTTTCTCAATAAAAGTCGAAAATTTGTTGGACTATCTTGGACCTTTCAGACGAAAGAAATTTTGCTTTAAGGTCGGTGTGAC
rvaser commented 5 years ago

That looks fine as well, hmm. Can you run the same for draft.fasta please? Also, please check the size of ONTmin_IT0.paf.

huandna commented 5 years ago

this is head -n 4 drat.fa:

>utg000001c
GCGCGATGCGGATTTTCAACACCAATCCACGCTTTTGCTTCAGCGGAACCTAGAATCCAG
CACTGGCGCTTCCGGGTCCTGGTGCCACTGAGTTGGTGGTGCCACTTTGCTTCTGACGGC
GCGGGGCCGCTTGTGTGACGCCGGCATCACGCACGGCCTGGGCTGCTAATCTGTTTTGAT

and the tail -n 4 draft.fa:

AGGCCTTGAGTCAGGTGCGAATTTTGTCGCTAATTTCAGGCGTACTTCCGCCAAGCCCTG
CGCTTTCACCTCTTCCGGCGCCTTCTTTCGGTGGTATCTTTCGAACGAAGTGATCGGCGA
GGAAACGCAGCAGCGCCTGCGTACGTGGACGCGGACCGGCGACCGGTACAAGCAGCGGGC
CACGGTGCTGCGGCGCCTGTGTCGTCT

I think the reason maybe \n in my draft.fa. and the size of ONTmin_IT0.paf is 23M (163988 lines),I will delete the \n to test again. haha:)

rvaser commented 5 years ago

The FASTA file can be wrapped, i.e. the new lines are not the problem. Well, that depends on which version of racon are you using. Which is it? :)

huandna commented 5 years ago

oh ,my version is v1.3.1

rvaser commented 5 years ago

Well, I have no idea then. Would you mind sharing the data with me via email so I can investigate further?

rvaser commented 5 years ago

You can also try and check if grep > reads.fasta | wc -l equals half of wc -l reads.fasta.

huandna commented 5 years ago

I find the issue grep > reads.fasta | wc -l get 164473 and wc -l reads.fasta get 328964,so it is my fault. I will recheck my fasta file.

Many thanks for your offer huanda

shiltemann commented 5 years ago

I ran into this same error (and solved it, but I just wanted to leave this here in case it's useful for anybody else in the future)

In my case it was because my fastq file contained reads of length 0. Performing a trimming step with minlen=1 (e.g. with trimmomatic) before running racon solved the issue for me.

damioresegun commented 5 years ago

I'm having this same issue. I haven't been able to figure it out. I'm using racon version 1.3.3, installed via git clone. I ran it as part of an iterative script on a cluster. Out of 6 datasets, 5 worked fine. One didnt. Command and error given are:

Command: ~/Tools/racon/build/bin/racon ../sks125VsHuman_unmapped.fastq sks125_readsVsCleanAssem.sam blob/sks125_clean.contigs.fasta -t 32 > ../sks125_racon1.fasta Error: [racon::Polisher::initialize] loaded target sequences 0.209 s [bioparser::FastqParser] error: invalid file format!

I've even gone back to see if it was something wrong with one my processing steps and its still the same.

rvaser commented 5 years ago

Hello, can you check whether there is a read of length 0 in your FASTQ file or the file end is truncated?

Sorry for the late response! Best regards, Robert

cahuparo commented 4 years ago

Hi Robert,

I have the same problem. Could you please help me out?

This is my racon command:

racon -t 16 trimmed_all_m54163.subreads.fastq read_map.sam assembly_all.contigs.fasta > racon.fasta

The error file: 

[racon::Polisher::initialize] loaded target sequences 1.919309 s
[racon::Polisher::initialize] loaded sequences 223.500546 s
terminate called after throwing an instance of 'std::invalid_argument'
  what():  [bioparser::SamParser] error: invalid file format!
Abort (core dumped)

So far I have troubleshooted by: 1) re-extracting reads from the subreads.bam that were larger than 100bp 2) running trimmomatic with minlen=1 and minlen=10 using the trimmed.fastq (above minlen=10)

I am using an HPC. Racon was installed using this https://anaconda.org/bioconda/racon.

Any help would be greatly appreciated.

Cheers,

Camilo

rvaser commented 4 years ago

Hello Camilo, could you tell me which command generated read_map.sam? The error indicates that something is off with it. The reads and assembly file are alright.

Best regards, Robert

cahuparo commented 4 years ago

Hi Robert,

Yes, this is the command from minimap2:

minimap2 -x map-pb -t 32 assembly_all.contigs.fasta all_m54163.subreads.fasta > read_map.sam

I realize I use the raw read data here instead of the trimmed reads. Do you think that is the problem?

Best,

Camilo

rvaser commented 4 years ago

Without option -a Minimap2 will produce a .paf file. Just run mv read_map.sam read_map.paf and run Racon with the new file.

cahuparo commented 4 years ago

Hi Robert,

I ran the following command:

racon -t 16 trimmed_all_m54163.subreads.fastq read_map.paf assembly_all39_contigs.fasta > racon.fasta

I did not get the same error above, but I got a different one after it run for a few minutes:

[racon::Polisher::initialize] loaded target sequences 1.115462 s
[racon::Polisher::initialize] loaded sequences 226.538331 s
[racon::Overlap::transmute] error: unequal lengths in sequence and overlap file for sequence m54163_180614_180502/4718753/2913_20215!

Do you have any suggestion?

Cheers,

Camilo

rvaser commented 4 years ago

Try using the original read file all_m54163.subreads.fasta or rerun Minimap2 with trimmed_all_m54163.subreads.fastq.

cahuparo commented 4 years ago

Thanks Robert! It is running. So do you recommend to stick to .paf format in future rounds?

Cheers,

Camilo

rvaser commented 4 years ago

However you want :) If you want .sam, run Minimap2 with -a.

damioresegun commented 4 years ago

I'm having this same issue. I haven't been able to figure it out. I'm using racon version 1.3.3, installed via git clone. I ran it as part of an iterative script on a cluster. Out of 6 datasets, 5 worked fine. One didnt. Command and error given are:

Command: ~/Tools/racon/build/bin/racon ../sks125VsHuman_unmapped.fastq sks125_readsVsCleanAssem.sam blob/sks125_clean.contigs.fasta -t 32 > ../sks125_racon1.fasta Error: [racon::Polisher::initialize] loaded target sequences 0.209 s [bioparser::FastqParser] error: invalid file format!

I've even gone back to see if it was something wrong with one my processing steps and its still the same.

Apologies for being so late. Yes it turns out there was an issue with one the reads in the fasta file. Just had to format it and it worked fine!

naahraissa commented 2 years ago

Hi Rvaser,

i have been very curious comparing racon with hypo polish. Hypo work well but i keep getting this problem:

[racon::Polisher::initialize] loaded target sequences 8.372787 s [racon::Polisher::initialize] loaded sequences 2478.189205 s terminate called after throwing an instance of 'std::invalid_argument' what(): [bioparser::SamParser] error: invalid file format Aborted (core dumped),

troubleshooting with raised issues doesn't help me:

please can you help me with some ideas

this is by command: i am using illumina paired end reads

minimap2 -t 64 consensus.fasta ${reads} > illumina.sam

racon -t 48 CsM2.fastq illumina.sam draft.fa > polished_Male3.racon.fa

Alternatively i tried overalapping the reads with generate and use a paf. file still it didn't work,

minimap2 -x ava-pb -t 8 reads.fa reads.fq > raw_hifiam.paf

Please i need your help. thanks,

Raissa

naahraissa commented 2 years ago

i used your script to generate a single file from the paired end reads as input for my sequence file illumina-Rmerge.py.txt

but sill not working

wwen-creat commented 2 years ago

Hi rvaser, I also run into the same error, and after tried the suggestions above, I think there might be something wrong with the Sam file, so i change my command "minimap2 -t 12 .fasta .fq.gz > .sam" to "minimap2 -t 12 .fasta .fq.gz -o .sam", then run "racon -m 8 -x -6 -g -8 -w 500 -t 4 .fq.gz .sam .fasta" it's working.

rvaser commented 2 years ago

If you want a .sam file from minimap2, you need to use option -a, otherwise you will get a .paf file. Racon uses the extension to know what it is parsing, either alignments in SAM format or mappings in PAF format.

greenmna commented 1 year ago

Hi rvaser, I also run into the same error, and after tried the suggestions above, I think there might be something wrong with the Sam file, so i change my command "minimap2 -t 12 .fasta .fq.gz > .sam" to "minimap2 -t 12 .fasta .fq.gz -o .sam", then run "racon -m 8 -x -6 -g -8 -w 500 -t 4 .fq.gz .sam .fasta" it's working.

I had tried everything else and this was the fix for me as well! For context, I'm using Minimap2 version 2.24 at time of posting. I am wondering if something with printing to STDOUT (default of minimap2) is causing formatting issues for Racon. Either way, directing an output using -o was the solution, so thank you for saving me the headache!