findAlleles get empty clone data about mixcr HOT 11 CLOSED

Hi, do you see the clones in the table before you run the findAlleles function?

from mixcr.

Actually not, when I run analysis, the assembleContigs step also detect 0 clones which is also weird:
Analysis date: Tue May 28 14:45:00 EDT 2024
Input file(s): ./result.clna
Output file(s): ./result.contigs.clns
Version: 4.3.2; built=Tue Apr 11 14:35:07 EDT 2023; rev=123d699964; lib=repseqio.v2.2
Command line arguments: assembleContigs --report ./result.assembleContigs.report.txt --json-report ./result.assembleContigs.report.json ./result.clna ./result.contigs.clns
Analysis time: 8.69m
Initial clonotype count: 336
Final clonotype count: 336 (100%)
Canceled assemblies: 0 (0%)
Number of premature termination assembly events, percent of number of initial clonotypes: 0.0 (0%)
Longest contig length: 615
Clustered variants: 0 (0%)
Reads in clustered variants: 0.0 (0%)
Reads in divided (newly created) clones: 0.0 (0%)
Clones with ambiguous letters in splitting region: 0 (0%)
Reads in clones with ambiguous letters in splitting region: 0.0 (0%)
Average number of ambiguous letters per clone with ambiguous letters in splitting region: NaN

from mixcr.

Can you please try running the analysis with the latest develop version. If you still see the issue, would it be possible to share the clns file? You can send it to [email protected]

from mixcr.

Hi, do you still see this issue?

from mixcr.

Hi! I am trying to run the latest version on remote server, but it said I don't have permission

from mixcr.

What error do you see? Is it a server message or a MiXCR error message?

from mixcr.

Actually when I try to run the latest version, it said [liu9756@owens-login04 mixcr]$ mixcr
Error: A JNI error has occurred, please check your installation and try again
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 ver
sion 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:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:621)

from mixcr.

what command do you try to run and what Java version do you have?

from mixcr.

Thanks! I update Java and it now successfully running!

from mixcr.

I use the latest version to run the analysis , but the assemble still display 0% clones, I will send the necessary files to the email.===================== report: assemble =====================
Analysis time: 306ms
Final clonotype count: 0
Reads used in clonotypes, percent of total: 0 (0%)
Average number of reads per clonotype: NaN
Reads dropped due to the lack of a clone sequence, percent of total: 1876 (0%)
Reads dropped due to a too short clonal sequence, percent of total: 0 (0%)
Reads dropped due to low quality, percent of total: 0 (0%)
Reads dropped due to failed mapping, percent of total: 0 (0%)
Reads dropped with low quality clones, percent of total: 0 (0%)
Aligned reads processed: 0
Reads used in clonotypes before clustering, percent of total: 0 (0%)
Number of reads used as a core, percent of used: 0 (NaN%)
Mapped low quality reads, percent of used: 0 (NaN%)
Reads clustered in PCR error correction, percent of used: 0 (NaN%)
Reads pre-clustered due to the similar VJC-lists, percent of used: 0 (NaN%)
Clonotypes dropped as low quality: 0
Clonotypes eliminated by PCR error correction: 0
Clonotypes pre-clustered due to the similar VJC-lists: 0
Clones dropped in post filtering: 0 (NaN%)
Reads dropped in post filtering: 0.0 (0%)
Alignments filtered by tag prefix: 0 (0%)
Pre-clone assembler report:
Number of input groups: 375
Number of input groups with no assembling feature: 375
Number of input alignments: 1876
Number of alignments with assembling feature: 0 (0%)
Number of output pre-clones: 0
Number of pre-clonotypes per group:
Number of assembling feature sequences in groups with zero pre-clonotypes: 0
Number of dropped pre-clones by tag suffix conflict: 0
Number of dropped alignments by tag suffix conflict: 0
Number of core alignments: 0 (0%)
Discarded core alignments: 0 (NaN%)
Empirically assigned alignments: 0 (0%)
Empirical assignment conflicts: 0 (0%)
Tag+VJ-gene empirically assigned alignments: 0 (0%)
VJ-gene empirically assigned alignments: 0 (0%)
Tag empirically assigned alignments: 0 (0%)
Number of ambiguous groups: 0
Number of ambiguous tag+V/J-gene combinations: 0
Ignored non-productive alignments: 0 (0%)
Unassigned alignments: 0 (0%)

from mixcr.

I will close this issue as it is directly connected to the #1713

from mixcr.