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Old 11-19-2014, 12:10 PM   #1
gupta.nitish
Junior Member
 
Location: Stony Brook, NY

Join Date: Nov 2014
Posts: 1
Default Need help: Unable to extract event data from fast5 file using poretool

We are trying to extract the event data from the set of Ecoli_R73 fast5 files using poretools. However, we are just getting the headers as given below..

>>poretools events ./downloads/LomanLabz_PC_Ecoli_K12_R7.3_2549_1_ch101_file3_strand.fast5

file strand mean start stdv length model_state model_level move p_model_state mp_model_state p_mp_model_state p_A p_Cp_G p_T raw_index



However we are able to successfully extract the event data from the Ecoli_R7_ONI fast5 files, shown below:

poretools events ./Ecoli_R7_ONI/flowcell_17/downloads/LomanLabz_PC_E.coli_MG1655_ONI_3058_1_ch1_file1_strand.fast5 | head -3

file strand mean start stdv length model_state model_level move p_model_state mp_model_state p_mp_model_state p_A p_Cp_G p_T raw_index

./Ecoli_R7_ONI/flowcell_17/downloads/LomanLabz_PC_E.coli_MG1655_ONI_3058_1_ch1_file1_strand.fast5 template54.3698260498 331.3562 1.5353363425 0.024 GGCG37.863502675 0 0.075828027313 GGCGA 0.0758280273130.172070730977 0.545313058662 0.264264061435 3.87242579997e-05 0

./Ecoli_R7_ONI/flowcell_17/downloads/LomanLabz_PC_E.coli_MG1655_ONI_3058_1_ch1_file1_strand.fast5 template54.7938415527 331.3802 1.28566063043 0.0124 GCGA36.7564960183 1 0.172004295914 GCGAT 0.1720042959140.450411898661 0.110056278207 0.435236090772 0.000106594134058 1

Why is this happening?

Thanks!
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Old 11-19-2014, 04:39 PM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,076
Default

It is possible that the copy you have for the K12 file is corrupt/incomplete. Have you tried to re-download that data from source?
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