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.
Input : 2023.10.19 23:29
Modified : 2024.02.21 15:08