1. Download & Verify Data¶
Lesson Objectives
- Inspect data with
md5(checksum verification)
This data is already downloaded and ready for you in ~/obss_2023/commandline/shell4b_data
Download with wget from a terminal client
Download via Web Browser (use locally)
- Data can be downloaded directly from this link which will download shell4b_data.tar.gz to Downloads directory
- If the above link fails, try this alternative .zip
Recap - Decompress downloaded tar.gz OR .zip
A TAR.GZ file is a combination of two different packaging algorithms. The first is tar, short for tape archive. It’s an old utility invented mainly for accurate data transfer to devices without their own file systems. A tar file (or tarball) contains files in a sequential format, along with metadata about the directory structure and other technical parameters.
It is useful to note that tar doesn’t compress the files in question, only packages them. Indeed, sometimes the resulting tarball can be of greater size due to padding. That’s where Gzip comes in. Gzip (denoted by a .gz file extension) is a compressed file format used to archive data to take up smaller space. Gzip uses the same compression algorithm as the more commonly known zip but can only be used on a single file. In short, Gzip compresses all the individual files and tar packages them in a single archive.
Decompressing the tar.gz file can be done with the built-in tar utility
x: Extract an archive.z: Compress the archive with gzip.v: Display progress in the terminal while creating the archive, also known as “verbose” mode. Thevis always optional in these commands, but it’s helpful.f: Allows you to specify the filename of the archive.
ZIP files can store multiple files using different compression techniques while at the same time supports storing a file without any compression. Each file is stored/compressed individually which helps to extract them, or add new ones, without applying compression or decompression to the entire archive.
Each file in a ZIP archive is represented as an individual entry consisting of a Local File Header followed by the compressed file data. The Directory at the end of the archive holds the references to all these file entries. ZIP file readers should avoid reading the local file headers and all types of file listing should be read from the Directory. This Directory is the only source for valid file entries in the archive as files can be appended towards the end of the archive as well. That is why if a reader reads local headers of a ZIP archive from the beginning, it may read invalid (deleted) entries as well those are not part of the Directory being deleted from archive.
The order of the file entries in the central directory need not coincide with the order of file entries in the archive.
Data Integrity¶
Data we download is the starting point of all future analyses and conclusions. Therefore it’s important to explicitly check the transferred data’s integrity with check‐sums. Checksums are very compressed summaries of data, computed in a way that even if just one bit of the data is changed the checksum will be different. As such, data integrity checks are also helpful in keeping track of data versions. Checksums facilitate reproducibility, as we can link a particular analysis and set of results to an exact version of data summarized by the data’s checksum value.
SHA and MD5 Checksums
Two most common checksum algorithms are MD5 and SHA (Specifically referring to SHA256)
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MD5 : cryptographic hash function algorithm that takes the message as input of any length and changes it into a fixed-length message of 16 bytes. MD5 algorithm stands for the message-digest algorithm.
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SHA : SHA-256 is a more secure and newer cryptographic hash function that was launched in 2000 as a new version of SHA functions and was adopted as Federal Information Processing Standards (FIPS) in 2002. It is allowed to use a hash generator tool to produce a SHA256 hash for any string or input value. Also, it generates 256 hash values, and the internal state size is 256 bit and the original message size is up to 264-1 bits.
To create checksums, we can pass arbitrary strings to the program md5sum (or sha256sum) through standard in
Checksums are reported in hexadecimal format, where each digit can be one of 16 characters: digits 0 through 9, and the letters a, b, c, d, e, and f. The trailing dash indicates this is the MD5 checksum of input from standard in. Checksums with file input can be done with md5usm filename .i.e.
Because it can get rather tedious to check each checksum individually, both md5sum and sha256sum has a convenient solution: Let's say that we want to verify the checksums for all of the .fasta files in the current directory. This can be done by creating and validating against a file containing the checksums of all the .fasta files.
fasta_checksums.md5contains the checksums for three .fasta files which were verified prior to uploading to github repo. This was generated by using the commandmd5sum *.fasta > fasta_checksums.md5- Run
md5sum -c fasta_checksums.md5and see whether all the .fasta files pass the verification-coption represent check
Applications will not trigger clear error messages for corrupted data
The following is an error message recorded on the log for a failed `bedtools genomecov` process ran on NeSI Mahuika cluster
```bash
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
```
* Doing a Google search for `std::bad_alloc` will take us to [this official reference documentation](https://en.cppreference.com/w/cpp/memory/new/bad_alloc)
* Expand the search a bit more with `BedTools std::bad_alloc` which will return [this reported issue on Biostars](https://www.biostars.org/p/377676/) as the first result.
std::bad_alloc is the C++ error code for when a new operator tries to allocate something, but fails. As C++ cannot dynamically allocate memory, the lack of memory is the most common cause.
So, it's quite difficult avoid the temptation to throw more memory at this process and re-run it. In fact, it was re-run with 0.5TB of memory as a sanity check which triggered the same error.
As it turned out, .bed file was corrupted . 🕵️♀️