Linux Major Troubleshooting [01-20]
Recommended Post: 【Operating System】 Lecture 1. Linux
1. cannot execute binary file: Exec format error
⑴ Cause 1. When the OS’s 64-bit / 32-bit architecture doesn’t match the file’s architecture
① Solution: Reinstall the OS according to the correct version
⑵ Cause 2. When the OS is arm-based
① Except for M1, most arm-based systems are used in smartphones
② Most publicly available programs are eventually based on amd architecture
③ Solution: It’s recommended to operate an amd-based OS on a regular PC
2. command not found
⑴ Cause 1. When the location of the file is not included in the environment settings
① Solution 1: Use the absolute path of the file
② Solution 2: Use the export command
3. permission denied
⑴ Cause 1. Due to chmod settings
① Abbreviation for change mode, used for permission management
② Types of users: user (u), group (g), others (o)
③ Types of permissions: read (r; 4), write (w; 2), execute (e; 1), rw- (4+2=6), r-x (4+1=5), rwx (4+2+1=7)
④ Method 1: Symbolic mode
○ Example 1: chmod u+x filename: Grant execute permission to the user
○ Example 2: chmod g-w filename: Remove write permission from the group
○ Example 3: chmod o=r filename: Set others’ permission to read-only
⑤ Method 2: Numeric mode
○ Example 1: chmod 755 filename: Set permissions to 7 for user, 5 for group, and 5 for others
⑥ Application 1: Setting permissions for an entire directory
○ Example 1: chmod -R 755 directory_name: Set 755 permissions for the entire directory_name
⑵ Cause 2. When the location of the file is not included in the environment settings
① Solution 1: Use the absolute path of the file
② Solution 2: Use the export command
4. packet_write_wait: Connection to 210.114.89.173 port 12604: Broken pipe
⑴ Cause 1. When the server closes the socket due to inactivity, causing an error as the client cannot connect
① Resolved by setting ServerAliveInterval
⑵ Cause 2. When the server detects a disconnection due to a brief interruption or reboot, causing an error
① Resolved by preventing the server from sending KeepAlive messages
⑶ Procedure
5. ERROR: There were no reads to process. Please check whether the read lengths in the input fastqs satisfy the minimum read length requirements for the chemistry.
⑴ Problem Situation: This problem can be encountered when running Space Ranger.
⑵ Cause 1. Typo: When there is an error in the fastq file name
⑶ Cause 2. When the expected R1 length is shorter than anticipated
6. [Directory] has only 43264kB remaining space available. To ignore this error, set MRO_DISK_SPACE_CHECK=disable in your environment.
⑴ Problem Situation: This occurred while running Linux/CPU-based pipelines such as Space Ranger.
⑵ Short-term Solution: export MRO_DISK_SPACE_CHECK=disable
⑶ Long-term Solution: Secure additional disk space
7. Log message: The input data has a very low rate of barcodes (0.0%) that match the selected slide type. Please check that your input data and slide serial number or chosen slide version are correct. Input: Sample NYU_GIST1 in “/data/jeongbinpark/231019_microbiota/GIST/Fastq”
⑴ Issue: When using Space Ranger, an error occurs in less than 10 seconds.
⑵ Solution: The Fastq files SRR20708363_1.fastq.gz and SRR20708363_2.fastq.gz need to be renamed to the format [sample_name]_S1_L001_R1_001.fastq.gz or ..._R2_001.fastq.gz (the sample name can be chosen arbitrarily). If SRR20708363_1.fastq.gz is named R1 and SRR20708363_2.fastq.gz is named R2, the above error occurs. However, if SRR20708363_1.fastq.gz is named R2 and SRR20708363_2.fastq.gz is named R1, it works properly.
⑶ Recommendation: As long as the slide serial number starts with V1, V4, V5, or H1, Space Ranger generally works well.
8. How to download files and folders from Onedrive using wget?
9. How to downloa a file from Dropbox using curl
⑴ Step 1. Click the 📎 button and set the sharing settings to public.
⑵ Step 2. Use the following command to download the file: curl -L -O {desired_filename} "{link_from_above}".
⑶ wget did not work successfully.
Input: 2023.10.19 23:29
Modified: 2024.02.21 15:08