Comments (15)
li1311139481
commented on July 1, 2024
Hi, I have the same problem, how did you solve it ?
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mizraelson
commented on July 1, 2024
What JAVA version do you have?
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li1311139481
commented on July 1, 2024
What JAVA version do you have?
My java version is
java version "1.8.0_391"
Java(TM) SE Runtime Environment (build 1.8.0_391-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.391-b13, mixed mode)
my mixcr version is 4.6.0.
I know that mixcr4.6.0 need openjdk>11.0. but when I install java11. I get
java.lang.RuntimeException: java.io.IOException: Input/output error
at com.milaboratory.o.cy.a(SourceFile:137)
at com.milaboratory.o.cB$a.run(SourceFile:420)
Caused by: java.io.IOException: Input/output error
at java.base/sun.nio.ch.FileDispatcherImpl.lock0(Native Method)
at java.base/sun.nio.ch.FileDispatcherImpl.lock(Unknown Source)
at java.base/sun.nio.ch.FileChannelImpl.lock(Unknown Source)
at java.base/java.nio.channels.FileChannel.lock(Unknown Source)
at com.milaboratory.o.cy.a(SourceFile:116)
... 1 more
License manager thread died.
License error: UnknownError
When i use java1.8
i get
Exception in thread "main" java.lang.UnsupportedClassVersionError: com/milaboratory/mixcr/cli/Main has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:756)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:473)
at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:359)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:635)
BTW. I do not have permission to install mixcr using docker and brew. I downloaded java myself, and I downloaded mixcr in conda with conda install -c milaboratories mixcr --no-deps
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mizraelson
commented on July 1, 2024
Can you please try downloading the latest Java from here and see if the error persists. Also, can you download MiXCR using the direct link: https://github.com/milaboratory/mixcr/releases/download/v4.6.0/mixcr-4.6.0.zip
And then run it as:
java -jar mixcr.jar -h
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li1311139481
commented on July 1, 2024
Can you please try downloading the latest Java from here and see if the error persists. Also, can you download MiXCR using the direct link: https://github.com/milaboratory/mixcr/releases/download/v4.6.0/mixcr-4.6.0.zip
And then run it as:
java -jar mixcr.jar -h
Thanks for your reply
I tried install java and mixcr according your instrction.
but i get error when i run java -jar mixcr.jar -h
[01:32:58][hlhuang][68]:mixcr$ java -jar "/cluster/facility/hlhuang/miniconda3/envs/mixcr/share/mixcr-4.6.0-0/mixcr.jar" -h
java.lang.RuntimeException: java.io.IOException: Input/output error
at com.milaboratory.o.cy.a(SourceFile:137)
at com.milaboratory.o.cB$a.run(SourceFile:420)
Caused by: java.io.IOException: Input/output error
at java.base/sun.nio.ch.UnixFileDispatcherImpl.lock0(Native Method)
at java.base/sun.nio.ch.UnixFileDispatcherImpl.lock(UnixFileDispatcherImpl.java:99)
at java.base/sun.nio.ch.FileChannelImpl.lock(FileChannelImpl.java:1487)
at java.base/java.nio.channels.FileChannel.lock(FileChannel.java:1240)
at com.milaboratory.o.cy.a(SourceFile:116)
... 1 more
License manager thread died.
License error: UnknownError
my java version:
[01:29:38][hlhuang][59]:mixcr$ javac -version
javac 21.0.1
[01:29:50][hlhuang][60]:mixcr$ java -version
java version "21.0.1" 2023-10-17 LTS
Java(TM) SE Runtime Environment (build 21.0.1+12-LTS-29)
Java HotSpot(TM) 64-Bit Server VM (build 21.0.1+12-LTS-29, mixed mode, sharing)
my ~/.bash_profile file
export JAVA_HOME=/cluster/facility/hlhuang/APP/java/jdk-21.0.1/
export JRE_HOME=${JAVA_HOME}/jre
export CLASSPATH=.:${JAVA_HOME}/lib:${JRE_HOME}/lib
export PATH=${JAVA_HOME}/bin:$PATH
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mizraelson
commented on July 1, 2024
It seems like there is an issue with permissions to the directory with license ~/.mi/.
Can you try running:
chmod -R 777 ~/.mi/
It can also be due to issues with disk mount or lack of storage space.
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li1311139481
commented on July 1, 2024
Thank you. Still not working
[12:26:40][hlhuang][213]:mixcr$ ls -lh ~/.mi
total 512
drwxrwxrwx 2 hlhuang hlhuang 3 Jan 3 00:22 com.milaboratory.mixcr.cli.Main
[12:26:58][hlhuang][214]:mixcr$ ls -lh ~/.mi/*
total 512
-rwxrwxrwx 1 hlhuang hlhuang 0 Jan 3 00:22 milicenashfingprintlock
[12:26:40][hlhuang][213]:mixcr$ ls -lh ~/.mi
total 512
drwxrwxrwx 2 hlhuang hlhuang 3 Jan 3 00:22 com.milaboratory.mixcr.cli.Main
[12:26:58][hlhuang][214]:mixcr$ ls -lh ~/.mi/*
total 512
-rwxrwxrwx 1 hlhuang hlhuang 0 Jan 3 00:22 milicenashfingprintlock
[12:27:04][hlhuang][215]:mixcr$ java -jar "/cluster/facility/hlhuang/APP/mixcr/mixcr.jar" activate-license
Please enter the license:
************************************ my license*****************************************
Checking the license...
java.lang.RuntimeException: java.io.IOException: Input/output error
at com.milaboratory.o.cy.a(SourceFile:137)
at com.milaboratory.o.cB$a.run(SourceFile:420)
Caused by: java.io.IOException: Input/output error
at java.base/sun.nio.ch.UnixFileDispatcherImpl.lock0(Native Method)
at java.base/sun.nio.ch.UnixFileDispatcherImpl.lock(UnixFileDispatcherImpl.java:99)
at java.base/sun.nio.ch.FileChannelImpl.lock(FileChannelImpl.java:1487)
at java.base/java.nio.channels.FileChannel.lock(FileChannel.java:1240)
at com.milaboratory.o.cy.a(SourceFile:116)
... 1 more
License manager thread died.
License Error:
UnknownError
null
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silvia1234567890
commented on July 1, 2024
Hi, I think your problem is related to the license.. I don't remember well how I solved this problem, because I tried different things.. If your problem is about the license:
I activated the license for academics through this link: https://licensing.milaboratories.com/
And then, in the terminal:
> mixcr activate-license
Please enter the license: ...
And in my case, I use mixcr through anaconda:
In the terminal (Mac) I just run:
> conda activate /Users/Silvia/anaconda3
> mixcr
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li1311139481
commented on July 1, 2024
I tried install mixcr using conda. and the same error happened.
I'm sure there's nothing wrong with my license, because i can activate mixcr in docker environment. but I don't like use docker.
(mixcr) [06:27:29][hlhuang][9]:~$ which mixcr
/cluster/facility/hlhuang/miniconda3/envs/mixcr/bin/mixcr
(mixcr) [06:27:31][hlhuang][10]:~$ mixcr -v
MiXCR v4.6.0 (built Sun Dec 10 03:48:42 CST 2023; rev=c9fafa41fe; branch=no_branch; host=fv-az520-378)
RepSeq.IO v2.4.0 (rev=5b5b4475b8)
MiLib v3.4.0 (rev=d42f072b23)
Built-in V/D/J/C library: repseqio.v4.0
Library search path:
- built-in libraries
- /cluster/home/hlhuang/.
(mixcr) [06:27:37][hlhuang][11]:~$ mixcr activate-license
Please enter the license:
Checking the license...
java.lang.RuntimeException: java.io.IOException: Input/output error
at com.milaboratory.o.cy.a(SourceFile:137)
at com.milaboratory.o.cB$a.run(SourceFile:420)
Caused by: java.io.IOException: Input/output error
at java.base/sun.nio.ch.UnixFileDispatcherImpl.lock0(Native Method)
at java.base/sun.nio.ch.UnixFileDispatcherImpl.lock(UnixFileDispatcherImpl.java:99)
at java.base/sun.nio.ch.FileChannelImpl.lock(FileChannelImpl.java:1487)
at java.base/java.nio.channels.FileChannel.lock(FileChannel.java:1240)
at com.milaboratory.o.cy.a(SourceFile:116)
... 1 more
License manager thread died.
License Error:
UnknownError
null
(mixcr) [06:27:54][hlhuang][12]:~$ which java
/cluster/facility/hlhuang/miniconda3/envs/mixcr/bin/java
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silvia1234567890
commented on July 1, 2024
I just checked and we have the same java version and mixcr version...
java version "1.8.0_391"
Java(TM) SE Runtime Environment (build 1.8.0_391-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.391-b13, mixed mode)
MiXCR v4.6.0 (built Sat Dec 09 20:48:42 CET 2023; rev=c9fafa41fe; branch=no_branch; host=fv-az520-378)
RepSeq.IO v2.4.0 (rev=5b5b4475b8)
MiLib v3.4.0 (rev=d42f072b23)
Built-in V/D/J/C library: repseqio.v4.0
Library search path:
- built-in libraries
- /Users/Silvia/.
Which java version do you have in conda?
Mine is:
openjdk 21.0.1 2023-10-17 LTS
OpenJDK Runtime Environment Zulu21.30+15-CA (build 21.0.1+12-LTS)
OpenJDK 64-Bit Server VM Zulu21.30+15-CA (build 21.0.1+12-LTS, mixed mode, sharing)
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li1311139481
commented on July 1, 2024
because i install mixcr using miniconda. so when I activate the environment of mixcr. it contain a openjdk. so my versionn like this:
(mixcr) [09:16:51][hlhuang][33]:20241231_B22GY5KLT3_U1244_ZF084_M_IV_TCRab$ which java
/cluster/facility/hlhuang/miniconda3/envs/mixcr/bin/java
(mixcr) [09:16:53][hlhuang][34]:20241231_B22GY5KLT3_U1244_ZF084_M_IV_TCRab$ java -version
openjdk version "21.0.1-internal" 2023-10-17
OpenJDK Runtime Environment (build 21.0.1-internal-adhoc.conda.src)
OpenJDK 64-Bit Server VM (build 21.0.1-internal-adhoc.conda.src, mixed mode, sharing)
(mixcr) [09:16:57][hlhuang][35]:20241231_B22GY5KLT3_U1244_ZF084_M_IV_TCRab$ javac -version
javac 21.0.1-internal
(mixcr) [09:17:39][hlhuang][36]:20241231_B22GY5KLT3_U1244_ZF084_M_IV_TCRab$ mixcr -v
MiXCR v4.6.0 (built Sun Dec 10 03:48:42 CST 2023; rev=c9fafa41fe; branch=no_branch; host=fv-az520-378)
RepSeq.IO v2.4.0 (rev=5b5b4475b8)
MiLib v3.4.0 (rev=d42f072b23)
Built-in V/D/J/C library: repseqio.v4.0
Library search path:
- built-in libraries
- /cluster/facility/hlhuang/zifeng001/ZF084_maxima_SSIV_bulk_TCRseq/20241231_B22GY5KLT3_U1244_ZF084_M_IV_TCRab/.
I have java version:
java version "21.0.1" 2023-10-17 LTS
Java(TM) SE Runtime Environment (build 21.0.1+12-LTS-29)
Java HotSpot(TM) 64-Bit Server VM (build 21.0.1+12-LTS-29, mixed mode, sharing)
openjdk version "1.8.0_131"
OpenJDK Runtime Environment (build 1.8.0_131-b12)
OpenJDK 64-Bit Server VM (build 25.131-b12, mixed mode)
but all java can't work
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mizraelson
commented on July 1, 2024
The issue appears to stem from the inability to lock a file in the .mi directory. This could be due to one of two reasons:
- The lock might have been placed by another process. To investigate this possibility, please try deleting the .mi directory and then rerunning
mixcr. - The filesystem in use might not support file locking. Could you specify where you are running mixcr? Are you using a standard filesystem like Mac's APFS, Linux, or Windows' NTFS, which generally support file locking? Or are you using a different filesystem such as FAT32, or a networked and distributed filesystem like GlusterFS, which typically do not support file locking?
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li1311139481
commented on July 1, 2024
@mizraelson Thanks for your reply
- I tried rm -rf ~/.mi. and rerun the code below. but not work
java -jar "/cluster/facility/hlhuang/APP/mixcr/mixcr.jar" activate-license
input my license
or using mixcr installed from conda
mixcr activate-license
input my license
I get same error
Checking the license...
java.lang.RuntimeException: java.io.IOException: Input/output error
at com.milaboratory.o.cy.a(SourceFile:137)
at com.milaboratory.o.cB$a.run(SourceFile:420)
Caused by: java.io.IOException: Input/output error
at java.base/sun.nio.ch.UnixFileDispatcherImpl.lock0(Native Method)
at java.base/sun.nio.ch.UnixFileDispatcherImpl.lock(UnixFileDispatcherImpl.java:99)
at java.base/sun.nio.ch.FileChannelImpl.lock(FileChannelImpl.java:1487)
at java.base/java.nio.channels.FileChannel.lock(FileChannel.java:1240)
at com.milaboratory.o.cy.a(SourceFile:116)
... 1 more
License manager thread died.
License Error:
UnknownError
null
- I am new to linux and I looked up some commands and I think my file system is XFS?
(mixcr) [01:07:00][hlhuang][154]:APP$ df -h
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 187G 71G 116G 38% /
devtmpfs 599G 0 599G 0% /dev
tmpfs 599G 240K 599G 1% /dev/shm
tmpfs 599G 179M 598G 1% /run
tmpfs 599G 0 599G 0% /sys/fs/cgroup
head1-10g0:/cluster 62T 46T 17T 74% /cluster
head1-10g0:/cluster/home 18T 456G 17T 3% /cluster/home
head1-10g0:/cluster/huanglab 108T 91T 17T 85% /cluster/huanglab
node3:/cluster2 99T 57T 42T 58% /cluster2
(mixcr) [01:21:30][hlhuang][155]:APP$ df -T
Filesystem Type 1K-blocks Used Available Use% Mounted on
/dev/sda1 xfs 195216252 73730788 121485464 38% /
devtmpfs devtmpfs 627174264 0 627174264 0% /dev
tmpfs tmpfs 627189376 240 627189136 1% /dev/shm
tmpfs tmpfs 627189376 183016 627006360 1% /run
tmpfs tmpfs 627189376 0 627189376 0% /sys/fs/cgroup
head1-10g0:/cluster nfs4 66542997504 48725812224 17817185280 74% /cluster
head1-10g0:/cluster/home nfs4 18295302144 478116864 17817185280 3% /cluster/home
head1-10g0:/cluster/huanglab nfs4 115289069568 97471884288 17817185280 85% /cluster/huanglab
node3:/cluster2 nfs4 105461161984 60475267072 44985894912 58% /cluster2
(mixcr) [01:23:25][hlhuang][156]:APP$ lsblk -f
NAME FSTYPE LABEL UUID MOUNTPOINT
sda
└─sda1 xfs c1761d3e-bbf1-461e-8a94-f7214206242e /
(mixcr) [01:23:48][hlhuang][157]:APP$ blkid
(mixcr) [01:23:56][hlhuang][158]:APP$ cat /etc/fstab
UUID=c1761d3e-bbf1-461e-8a94-f7214206242e / xfs defaults 0 0
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mizraelson
commented on July 1, 2024
From your output, I see that your home folder resides on nfs network drive.
Please provide the output of the:
pwdandls -lacommands in the terminal after you log into the servermountcommand
It seems that it's a permission error.
from mixcr.
li1311139481
commented on July 1, 2024
From your output, I see that your home folder resides on
nfsnetwork drive. Please provide the output of the:
pwdandls -lacommands in the terminal after you log into the servermountcommandIt seems that it's a permission error.
[11:45:01][hlhuang][1]:~$ pwd
/cluster/home/hlhuang
[11:45:04][hlhuang][2]:~$ ls -la
total 500
drwx------ 41 hlhuang hlhuang 73 Jan 5 23:44 .
drwxr-xr-x 69 root root 69 Nov 4 15:14 ..
drwxrwxr-x 3 hlhuang hlhuang 3 Sep 24 2022 .anaconda_backup
drwx------ 4 hlhuang hlhuang 4 Jan 2 01:59 .apptainer
-rw------- 1 hlhuang hlhuang 207213 Jan 5 02:03 .bash_history
-rw-r--r-- 1 hlhuang hlhuang 18 Aug 3 2016 .bash_logout
-rw-r--r-- 1 hlhuang hlhuang 417 Jan 4 13:02 .bash_profile
-rw------- 1 hlhuang hlhuang 12288 Aug 14 2022 .bash_profile.swo
-rw------- 1 hlhuang hlhuang 12288 Aug 14 2022 .bash_profile.swp
-rw-rw-r-- 1 hlhuang hlhuang 4458 Jan 2 00:15 .bashrc
-rw-r--r-- 1 hlhuang hlhuang 12288 Aug 25 2022 .bashrc.swo
-rw-r--r-- 1 hlhuang hlhuang 12288 Aug 4 2022 .bashrc.swp
drwxr-xr-x 6 hlhuang hlhuang 9 Nov 7 00:04 bin
drwxr-xr-x 19 hlhuang hlhuang 20 Nov 9 17:40 .cache
drwxrwxr-x 2 hlhuang hlhuang 34 Apr 4 2023 code
drwxrwxr-x 4 hlhuang hlhuang 5 Aug 18 11:14 .conda
-rw-rw-r-- 1 hlhuang hlhuang 78 Sep 3 02:19 .condarc
-rw------- 1 hlhuang hlhuang 12288 Aug 10 2022 .condarc.swo
-rw------- 1 hlhuang hlhuang 12288 Aug 10 2022 .condarc.swp
drwxr-x--- 16 hlhuang hlhuang 16 Nov 17 2022 .config
drwx------ 3 hlhuang hlhuang 3 Aug 9 2022 .dbus
drwxr-xr-x 3 hlhuang hlhuang 3 Oct 19 2022 Desktop
drwx------ 3 hlhuang hlhuang 4 Oct 19 2022 Downloads
-rw------- 1 hlhuang hlhuang 16 Aug 10 2022 .esd_auth
-rw-rw-r-- 1 hlhuang hlhuang 78 Nov 6 2022 .gitconfig
drwxrwxr-x 3 hlhuang hlhuang 3 Nov 17 2022 go
drwxrwxr-x 4 hlhuang hlhuang 5 Apr 3 2023 gsea_home
drwxrwxr-x 3 hlhuang hlhuang 6 Jan 13 2023 igv
drwxrwxr-x 2 hlhuang hlhuang 3 Jan 13 2023 .igv
lrwxrwxrwx 1 hlhuang hlhuang 35 Feb 15 2023 .ipython -> /cluster/facility/hlhuang/.ipython/
drwxrwxr-x 4 hlhuang hlhuang 4 Oct 27 2022 .java
drwx------ 4 hlhuang hlhuang 6 Oct 14 12:17 .jupyter
-rw-rw-r-- 1 hlhuang hlhuang 39392 Nov 6 21:44 jupyter_lab_config1.py
-rw-rw-r-- 1 hlhuang hlhuang 37752 May 7 2023 jupyter_lab_config.py
-rw------- 1 hlhuang hlhuang 306 Jul 5 2023 .lesshst
drwxr-x--- 5 hlhuang hlhuang 5 Dec 22 2022 .local
drwxrwxr-x 3 hlhuang hlhuang 3 Apr 22 2023 .matplotlib
drwxrwxr-x 3 hlhuang hlhuang 3 Jan 4 13:04 .mi
-rw-r--r-- 1 hlhuang hlhuang 619 Dec 24 10:58 mi.license
drwxrwxr-x 3 hlhuang hlhuang 3 Apr 22 2023 .mozilla
drwx------ 2 hlhuang hlhuang 3 Aug 10 2022 .ncbi
-rw-rw-r-- 1 hlhuang hlhuang 705 Feb 3 2023 .ncbirc
drwxrwxr-x 7 hlhuang hlhuang 8 Apr 9 2023 .nextflow
drwxrwxr-x 4 hlhuang hlhuang 5 Oct 20 2022 .npm
drwxrwxr-x 2 hlhuang hlhuang 4 Jun 26 2022 .oracle_jre_usage
drwxrw---- 3 hlhuang hlhuang 3 Sep 13 2022 .pki
-rw------- 1 hlhuang hlhuang 3180 Oct 14 03:40 .python_history
drwxr-xr-x 3 hlhuang hlhuang 3 Jul 18 2022 .R
-rw-rw-r-- 1 hlhuang hlhuang 10099 Sep 7 09:59 .radian_history
drwxrwxr-x 2 hlhuang hlhuang 14 Apr 23 2023 rgtdata
-rw------- 1 hlhuang hlhuang 66 Aug 25 17:09 .Rhistory
drwxrwxr-x 3 hlhuang hlhuang 3 Aug 25 2022 RNAseq
-rw------- 1 hlhuang hlhuang 12288 Oct 19 2022 .rserver.conf.swp
drwxr-xr-x 20 hlhuang hlhuang 27 Dec 29 23:53 .rstudio
-rw-rw-r-- 1 hlhuang hlhuang 44 Sep 5 2022 .screenrc
drwxrwxr-x 11 hlhuang hlhuang 11 Jul 26 2022 .sdkman
drwx------ 3 hlhuang hlhuang 3 Nov 8 12:43 .singularity
drwx------ 2 hlhuang hlhuang 8 Aug 19 01:37 .ssh
drwxrwxr-x 3 hlhuang hlhuang 5 May 8 2023 ssh_copy
-rwxrwxr-x 1 hlhuang hlhuang 8672 Nov 6 21:56 tempCodeRunnerFile
-rw-rw-r-- 1 hlhuang hlhuang 234 Nov 6 21:56 tempCodeRunnerFile.c
-rwS--s--- 1 hlhuang hlhuang 0 Nov 6 21:56 test.db
drwxrwxr-x 6 hlhuang hlhuang 6 Oct 19 00:35 .transfer_client
-rw------- 1 hlhuang hlhuang 4172 Aug 10 2022 .viminfo.tmp
drwxrwxr-x 2 hlhuang hlhuang 2 Nov 11 2022 .virtual_documents
drwxrwxr-x 2 hlhuang hlhuang 5 Apr 22 2023 .vscode-R
drwxrwxr-x 5 hlhuang hlhuang 20 Dec 25 01:06 .vscode-server
-rw-rw-r-- 1 hlhuang hlhuang 320 Oct 3 11:48 .wget-hsts
-rw-rw-r-- 1 hlhuang hlhuang 0 Jun 27 2023 withCallingHandlers
drwxrwxr-x 9 hlhuang hlhuang 9 Nov 18 2022 work
-rw------- 1 hlhuang hlhuang 1020 Jan 5 23:44 .Xauthority
drwxrwxr-x 4 hlhuang hlhuang 4 Oct 6 14:23 .yarn
-rw-rw-r-- 1 hlhuang hlhuang 717 Aug 14 2022 .zshrc
[11:45:08][hlhuang][3]:~$ mount
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
devtmpfs on /dev type devtmpfs (rw,nosuid,size=627174264k,nr_inodes=156793566,mode=755)
securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)
tmpfs on /run type tmpfs (rw,nosuid,nodev,mode=755)
tmpfs on /sys/fs/cgroup type tmpfs (ro,nosuid,nodev,noexec,mode=755)
cgroup on /sys/fs/cgroup/systemd type cgroup (rw,nosuid,nodev,noexec,relatime,xattr,release_agent=/usr/lib/systemd/systemd-cgroups-agent,name=systemd)
pstore on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime)
cgroup on /sys/fs/cgroup/pids type cgroup (rw,nosuid,nodev,noexec,relatime,pids)
cgroup on /sys/fs/cgroup/freezer type cgroup (rw,nosuid,nodev,noexec,relatime,freezer)
cgroup on /sys/fs/cgroup/cpu,cpuacct type cgroup (rw,nosuid,nodev,noexec,relatime,cpuacct,cpu)
cgroup on /sys/fs/cgroup/perf_event type cgroup (rw,nosuid,nodev,noexec,relatime,perf_event)
cgroup on /sys/fs/cgroup/net_cls,net_prio type cgroup (rw,nosuid,nodev,noexec,relatime,net_prio,net_cls)
cgroup on /sys/fs/cgroup/cpuset type cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)
cgroup on /sys/fs/cgroup/hugetlb type cgroup (rw,nosuid,nodev,noexec,relatime,hugetlb)
cgroup on /sys/fs/cgroup/devices type cgroup (rw,nosuid,nodev,noexec,relatime,devices)
cgroup on /sys/fs/cgroup/memory type cgroup (rw,nosuid,nodev,noexec,relatime,memory)
cgroup on /sys/fs/cgroup/blkio type cgroup (rw,nosuid,nodev,noexec,relatime,blkio)
configfs on /sys/kernel/config type configfs (rw,relatime)
/dev/sda1 on / type xfs (rw,relatime,attr2,inode64,noquota)
systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=30,pgrp=1,timeout=0,minproto=5,maxproto=5,direct)
mqueue on /dev/mqueue type mqueue (rw,relatime)
hugetlbfs on /dev/hugepages type hugetlbfs (rw,relatime)
debugfs on /sys/kernel/debug type debugfs (rw,relatime)
nfsd on /proc/fs/nfsd type nfsd (rw,relatime)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw,relatime)
head1-10g0:/cluster on /cluster type nfs4 (rw,relatime,vers=4.0,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,port=0,timeo=600,retrans=2,sec=sys,clientaddr=10.1.2.1,local_lock=none,addr=10.1.0.1)
head1-10g0:/cluster/home on /cluster/home type nfs4 (rw,relatime,vers=4.0,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,port=0,timeo=600,retrans=2,sec=sys,clientaddr=10.1.2.1,local_lock=none,addr=10.1.0.1)
head1-10g0:/cluster/huanglab on /cluster/huanglab type nfs4 (rw,relatime,vers=4.0,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,port=0,timeo=600,retrans=2,sec=sys,clientaddr=10.1.2.1,local_lock=none,addr=10.1.0.1)
node3:/cluster2 on /cluster2 type nfs4 (rw,relatime,vers=4.0,rsize=1048576,wsize=1048576,namlen=255,hard,proto=tcp,port=0,timeo=600,retrans=2,sec=sys,clientaddr=10.0.2.1,local_lock=none,addr=10.0.2.3)
binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,relatime)
fusectl on /sys/fs/fuse/connections type fusectl (rw,relatime)
from mixcr.
Related Issues (20)
- postanalysis NullPointerException HOT 9
- Somatic hypermutation analysis HOT 1
- Analysis of single chain Fragment variable (scFv) HOT 1
- Error exportPlots shmTrees - Duplicate library: repseqio.v4.0_with_found_alleles:10090 HOT 2
- transitioning from postanalysis to exportPlots HOT 1
- Somatic Hypermutation Status of IGHV status HOT 2
- Question about filtering reads prior to Mixcr HOT 1
- Preset for long-read RNAseq with cell barcode HOT 1
- How to perform MiXCR on my spatial TCR data
- The problem of mixcr exportPlots shmTrees HOT 1
- The majority of results in 'clones_TR[A|B].tsv' are "region_not_covered" HOT 1
- allVHitsWithScore allDHitsWithScore allJHitsWithScore allCHitsWithScore HOT 1
- FASTQ and BAM give discordant results HOT 4
- Help with TCR-seq alignment rate
- findAlleles get empty clone data HOT 3
- Rhapsody BCR+TCR full length data input HOT 2
- Generating all all_contig_annotations.json to run enclone after MiXCR
- Postanalysis output explanation
- `Feature for allele search doesn't intersect JGene` error when running `findAlleles` HOT 1
- Runtime error of "Can't apply step BuildingInitialTrees" when running findShmTrees
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