Add answers to Linux CLI for Bioinformatics training

Linux for Bioinformatics/answers.md

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+# Answers to questions from "Linux for Bioinformatics"
+
+**Q1: What is your home directory?**
+
+A: The home directory for the user `ubuntu` is `/home/ubuntu`.
+
+**Q2: What is the output of the `ls` command in the `my_folder/` directory?**
+
+A: The output of the `ls` command in the `my_folder/` directory is:
+
+```shell
+hello_world.txt
+```
+**Q3: What is the output of each `ls` command?**
+
+- `ls my_folder`: (no output, the directory is empty)
+- `ls my_folder2`: `hello_world.txt`
+
+**Q4: What is the output of each `ls` command?**
+
+- `ls my_folder`: (no output, the directory is empty)
+- `ls my_folder2`: (no output, the directory is empty)
+- `ls my_folder3`: `hello_world.txt`
+
+**Q5: What editor did you use and what was the command to save your file changes?**
+
+A: I used the `nano` editor. The command to save my file changes was `Ctrl + O` followed by `Enter`, and then `Ctrl + X` to exit the editor.
+
+**Q6. What is the error?**
+
+A : The error encountered is Permission denied (publickey).
+The error occurs because `sudouser` does not have the SSH key required for login.
+
+**Q7. What was the solution?**
+
+A : To enable password and keyboard-interactive authentication for SSH on your server, you need to edit the SSH configuration file (`/etc/ssh/sshd_config`) by setting `PasswordAuthentication yes` and `KbdInteractiveAuthentication yes`. After saving these changes, restart the SSH service with `systemctl restart ssh.service` to apply them. Then, exit your current session and log out. Finally, SSH into the remote server using the command `ssh sudouser@54.196.151.172`. This process ensures that the server allows password and keyboard-interactive authentication methods.
+
+
+**Q8: What does the `sudo docker run` part of the command do? and what does the `salmon swim` part of the command do?**
+
+- **`sudo docker run`**: This part of the command starts a Docker container. It creates a new container from the specified image (`combinelab/salmon`), and runs the specified command within that container. In this case, it runs the `salmon` command within the `combinelab/salmon` Docker image.
+
+- **`salmon swim`**: This part of the command is the specific command run inside the Docker container. `salmon swim` is a command in the `salmon` software that prints version information and other details about the `salmon` tool.
+
+**Q9. What is the output of this command?** `sudo ls /root`
+
+[sudo] password for serveruser:
+serveruser is not in the sudoers file. 
+
+**Q10. What is the output of `flask --version`?**
+
+A: The output is:
+```shell
+Python 3.10.14
+Flask 3.0.3
+Werkzeug 3.0.3
+```
+
+**Q11. What is the output of `mamba -V`?**
+
+A: The output is:
+```shell
+mamba 1.5.8
+conda 24.3.0
+```
+
+**Q12. What is the output of `which python`?**
+
+   The output :
+   ```shell
+   /home/serveruser/mambaforge/envs/py27/bin/python
+   ```
+
+**Q13. What is the output of `which python` now?**
+
+   The output :
+   ```shell
+   /home/serveruser/mambaforge/bin/python
+   ```
+
+**Q14. What is the output of `salmon -h`?**
+
+The output :
+
+```shell
+salmon v1.4.0
+
+Usage:  salmon <SUBCOMMAND> [options]
+
+Subcommands:
+    index       Create a quasi-mapping-based index
+    quant       Quantify a set of reads
+    alevin      Quantify barcoded (single-cell) reads
+    swim        Perform super-secret operation
+    ... (additional commands and options)
+```
+
+**Q15. What does the `-o athal.fa.gz` part of the command do?**
+
+A: The `-o athal.fa.gz` part of the command specifies the output file name. It tells `curl` to save the downloaded file as `athal.fa.gz`.
+
+**Q16. What is a `.gz` file?**
+
+A: A `.gz` file is a file compressed using the gzip compression algorithm. It is commonly used to reduce the size of files for storage and transfer.
+
+**Q17. What does the `zcat` command do?**
+
+A: The `zcat` command reads compressed files (with the `.gz` extension) and outputs their uncompressed contents to the standard output.
+
+**Q18. What does the `head` command do?**
+
+A: The `head` command displays the first part of a file. By default, it shows the first 10 lines, but this can be adjusted with a numerical argument.
+
+**Q19. What does the number `100` signify in the command?**
+
+A: The number `100` specifies that the `head` command should display the first 100 lines of the uncompressed file.
+
+**Q20. What is `|` doing?**
+
+A: The `|` (pipe) operator takes the output of the command on its left (`zcat athal.fa.gz`) and passes it as input to the command on its right (`head -n 100`).
+
+**Q21. What is a `.fa` file? What is this file format used for?**
+
+A: A `.fa` file is a FASTA file, a text-based format for representing nucleotide sequences or peptide sequences. Each sequence is represented by a series of lines, with the first line starting with a `>` character followed by a sequence identifier and description, and the subsequent lines containing the sequence itself. This format is commonly used in bioinformatics for storing sequence data.
+
+**Q22. What format are the downloaded sequencing reads in?**
+
+A: The downloaded sequencing reads are in SRA format, which is a binary format used by NCBI for storing high-throughput sequencing data.
+
+**Q23. What is the total size of the disk?**
+
+A:  6.8G
+
+Filesystem      Size  Used Avail Use% Mounted on
+/dev/root       6.8G  5.3G  1.5G  80% /
+tmpfs           479M     0  479M   0% /dev/shm
+tmpfs           192M  936K  191M   1% /run
+tmpfs           5.0M     0  5.0M   0% /run/lock
+/dev/xvda16     881M   76M  744M  10% /boot
+/dev/xvda15     105M  6.1M   99M   6% /boot/efi
+tmpfs            96M   12K   96M   1% /run/user/1000
+tmpfs            96M   12K   96M   1% /run/user/1002
+
+**Q24. How much space is remaining on the disk?**
+
+A: 1.5G
+
+**Q25. What went wrong?**
+
+A: The error message indicates that there is not enough storage space available to complete the fastq-dump process.
+
+
+(2024-05-23T20:37:16 fastq-dump.2.11.0 err: storage exhausted while writing file within file system module - system bad file descriptor error fd='5'
+
+=============================================================
+An error occurred during processing.
+A report was generated into the file '/home/serveruser/ncbi_error_report.txt'.
+If the problem persists, you may consider sending the file
+to 'sra-tools@ncbi.nlm.nih.gov' for assistance.
+=============================================================
+
+fastq-dump quit with error code 3
+(sraEnv) serveruser@ip-172-31-31-230:~$)
+
+**Q26: What was your solution?**
+
+A: Compress the output using gzip to save disk space during conversion.
+
+1. **Delete the Partially-Generated `.fastq` File**:
+   ```bash
+   rm SRR074122.fastq
+   ```
+
+2. **Modify the `fastq-dump` Command**:
+   Use gzip compression to reduce disk space usage during conversion:
+   ```bash
+   fastq-dump --gzip SRR074122
+   ```