Error in converting fast5 to slow5

[dsaha0295]

Hello,

Thank you for developing this tool. We've been having some trouble with converting our fast5 files to the slow5 format. We are using the following command:

name=FAS65713
fast5="$wd"/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5/
blow5="$wd"/saha.d/projects/RNA_meth/data/FAS65713_blow5
fastq="$wd"/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/FAS65713_pass_ac2853db_b43e8763.fastq

slow5tools f2s "$fast5" -d "$blow5" -p 8

This is the error we receive:

list_all_items] Looking for '*.fast5' files in /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5/
[f2s_main] 199 fast5 files found - took 0.087s
[f2s_main] Just before forking, peak RAM = 0.000 GB
[f2s_iop] 8 proceses will be used.
[f2s_iop] Spawning 8 I/O processes to circumvent HDF hell.
[fast5_attribute_itr::ERROR] Bad fast5: Attribute Raw/tracked_scaling_scale in /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_108.fast5 is unexpected. Please report this with an example FAST5 file at 'https://github.com/hasindu2008/slow5tools/issues' for us to investigate.
[read_fast5::ERROR] Bad fast5: Could not iterate over the read groups in the fast5 file /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_108.fast5.
[f2s_child_worker::ERROR] Bad fast5: Could not read contents of the fast5 file '/storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_108.fast5'.
[fast5_attribute_itr::ERROR] Bad fast5: Attribute Raw/tracked_scaling_scale in /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_1.fast5 is unexpected. Please report this with an example FAST5 file at 'https://github.com/hasindu2008/slow5tools/issues' for us to investigate.
[read_fast5::ERROR] Bad fast5: Could not iterate over the read groups in the fast5 file /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_1.fast5.
[f2s_child_worker::ERROR] Bad fast5: Could not read contents of the fast5 file '/storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_1.fast5'.
[fast5_attribute_itr::ERROR] Bad fast5: Attribute Raw/tracked_scaling_scale in /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_189.fast5 is unexpected. Please report this with an example FAST5 file at 'https://github.com/hasindu2008/slow5tools/issues' for us to investigate.
[read_fast5::ERROR] Bad fast5: Could not iterate over the read groups in the fast5 file /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_189.fast5.
[f2s_child_worker::ERROR] Bad fast5: Could not read contents of the fast5 file '/storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_189.fast5'.
[fast5_attribute_itr::ERROR] Bad fast5: Attribute Raw/tracked_scaling_scale in /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_184.fast5 is unexpected. Please report this with an example FAST5 file at 'https://github.com/hasindu2008/slow5tools/issues' for us to investigate.
[read_fast5::ERROR] Bad fast5: Could not iterate over the read groups in the fast5 file /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_184.fast5.
[f2s_child_worker::ERROR] Bad fast5: Could not read contents of the fast5 file '/storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_184.fast5'.
[fast5_attribute_itr::ERROR] Bad fast5: Attribute Raw/tracked_scaling_scale in /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_19.fast5 is unexpected. Please report this with an example FAST5 file at 'https://github.com/hasindu2008/slow5tools/issues' for us to investigate.
[read_fast5::ERROR] Bad fast5: Could not iterate over the read groups in the fast5 file /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_19.fast5.
[f2s_child_worker::ERROR] Bad fast5: Could not read contents of the fast5 file '/storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_19.fast5'.
[fast5_attribute_itr::ERROR] Bad fast5: Attribute Raw/tracked_scaling_scale in /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_107.fast5 is unexpected. Please report this with an example FAST5 file at 'https://github.com/hasindu2008/slow5tools/issues' for us to investigate.
[read_fast5::ERROR] Bad fast5: Could not iterate over the read groups in the fast5 file /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_107.fast5.
[f2s_child_worker::ERROR] Bad fast5: Could not read contents of the fast5 file '/storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_107.fast5'.
[fast5_attribute_itr::ERROR] Bad fast5: Attribute Raw/tracked_scaling_scale in /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_163.fast5 is unexpected. Please report this with an example FAST5 file at 'https://github.com/hasindu2008/slow5tools/issues' for us to investigate.
[read_fast5::ERROR] Bad fast5: Could not iterate over the read groups in the fast5 file /storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_163.fast5.
[f2s_child_worker::ERROR] Bad fast5: Could not read contents of the fast5 file '/storage1/fs1/christophermaher/Active/maherlab/sidizhao/circ_rna/long_read/m6a_methlytion_direct_rna/hct116_mettl3_kd_crispr/fast5//FAS65713_pass_ac2853db_b43e8763_163.fast5'.
[f2s_iop] Child process 10 exited with status=1.

A sample file can be downloaded here: https://wustl.box.com/s/cdrwq1vlh9cdyj1x0vx7j2pt4v4n7yy8 Any help and insight would be greatly appreciated. Thank you, dsaha0295@gmail.com sidizhao94@gmail.com

[hasindu2008]

This was a recent change ONT made to the FAST5 format and was addressed in a newer version of slow5tools. Could you check which version of slow5tools you are using? I suggest trying with the latest version.

[hasindu2008]

@dsaha0295 Has your problem been solved?

[hasindu2008]

Since there is no response I am closing the issue for now. Feel free to reopen if it still persists.