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Awk orders to specify the delimiter output string / what is the error report encountered when using bgzip? I believe many inexperienced people are at a loss about this. Therefore, this article summarizes the causes and solutions of the problem. Through this article, I hope you can solve this problem.

Problems encountered by awk in specifying character segmentation strings and specifying delimiter output strings

Using blasr software to compare the third generation sequencing data to the reference sequence

Blasr longreads.fastq reference.fasta-- nproc 16 > blasr.out

Partial output result

M54155 "170415" 100314 reference 5309390 "25118" 26816 ash 01698" 1-3020 75.3097 127858 128847 510317 3 1182

M54155 170415 100314 reference 5243602 09942 reference 0 1-1076 17916 18284 510317 8946 9296 9742

M54155 "170415" 100314 reference 5440071 * 09295 reference 00-1122 470798 471063 510317 0267 9295 5

This place does not know why the ID of reads has been added to the latter part. If you use this ID to extract the reads on the comparison, you will not get the result.

You can use the awk command to remove the ending.

Reference link https://blog.csdn.net/liangbilin/article/details/108593296

Cat blasr.out | awk'{print $1}'| awk-F'/'- v OFS= "/"'{print $1

-F specifies the delimiter of the input file-v OFS specifies the delimiter of the output file

Error report encountered by bgzip and its solution

There is no bgzip command on this server. I use conda to install it.

Conda install tabix

This is installed with version 0.2.6.

When unzipping fastq files

Bgzip-d pacbio.sequel.fastq.gz

Encounter an error report

Error: 2

Then I uninstall and reinstall 0.2.5 and try it.

Conda uninstall tabix

Conda install tabix=0.2.5

Decompress again and report an error.

Error: invalid block header

I don't know why I reported the error above. After searching for it, I saw that someone said that after installing htslib, I could use bgzip directly. I tried it.

Conda uninstall tabix

Conda install htslib

Sure enough, if you use bgzip to decompress this time, you will get it right.

After reading the above, have you mastered the awk command to specify the delimiter output string / / how to report the error encountered by bgzip? If you want to learn more skills or want to know more about it, you are welcome to follow the industry information channel, thank you for reading!

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