Java error at MiTFi step

[linzhi2013]

Java error at MiTFi step

[linzhi2013]

Dear AlesBucek,

Thanks for your feedback!

Can you tell me that what was the way you used MitoZ? If you installed MitoZ from source code, did you run source activate mitozEnv firstly when you ran the MitoZ commands?

It seems to be the problem of Java. Could you please check which java you used, e.g. which java, it should be from the mitozEnv environment.

Cheers,
Guanliang

[AlesBucek]

Dear Guanliang,
thanks for your fast response.
I indeed installed MitoZ from source code following instructions in INSTALL.md, paragraph 3.
I run MitoZ from the mitozEnv environment activated by source activate mitozEnv
(Note that the Assemble module runs without any problems)
Java seen from within the environment is

~/anaconda_ete/envs/mitozEnv/bin/java

Thanks and cheers,
Ales

[linzhi2013]

HI Ales,

I tried the following:

$ source activate mitozEnv
$ cd release_MitoZ_v2.3/bin/annotate/mitfi
$ java -Xmx2048m -jar mitfi.jar -cores 1 -code 5 -evalue 0.001 -onlycutoff  mitogenome.fasta > mitogenome.fasta.trna

The output is:

MiTFi - mitochondrial tRNA finder v0.1
 #RESULTS (cutoff evalue: 0.001)
#22 hits

My platform information:

$ cat /etc/os-release

NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

$ uname -r

3.10.0-957.12.2.el7.x86_64

Could you have a try as above?

I don't know why it did not work for you.

Cheers,
Guanliang

[AlesBucek]

Hi Gunliang,
thanks for the instructions.
Running just mitfi.jar as you specified from the MitoZ folder reproduces for me the Java error:

MiTFi - mitochondrial tRNA finder v0.1
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: begin 2, end 0, length 14
	at java.base/java.lang.String.checkBoundsBeginEnd(String.java:3319)
	at java.base/java.lang.String.substring(String.java:1874)
	at mitfi.Main.main(Main.java:221)

My system is very similar to yours:

$ cat /etc/os-release
NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

uname -r
3.10.0-327.el7.x86_64

I'll check with the system administrators if they have an explanation but if you have any suggestions or just general idea what might be wrong I'd be thankful for that.
Cheers,
Ales

[AlesBucek]

The version of java in the environment is:
~/anaconda_ete/envs/mitozEnv/bin/java -version

openjdk version "11.0.1" 2018-10-16 LTS
OpenJDK Runtime Environment Zulu11.2+3 (build 11.0.1+13-LTS)
OpenJDK 64-Bit Server VM Zulu11.2+3 (build 11.0.1+13-LTS, mixed mode)

Is this ok?

[linzhi2013]

I think your java is fine.

Here is my java:

$ source activate mitozEnv

$ which java
~/soft/bio/Miniconda3/envs/mitozEnv/bin/java

$ java --version
openjdk 11.0.1 2018-10-16 LTS
OpenJDK Runtime Environment Zulu11.2+3 (build 11.0.1+13-LTS)
OpenJDK 64-Bit Server VM Zulu11.2+3 (build 11.0.1+13-LTS, mixed mode)

[linzhi2013]

Do not if your download is complete.

Check if your md5sum is the same as mine:

$ cd release_MitoZ_v2.3/bin/annotate/mitfi/
$ md5sum mitfi.jar
62c373a654aded66c3e5c5459f67eef5  mitfi.jar
$ md5sum cmsearch
8b0fc1e7b9fc65208050630c9a848ac4  cmsearch
$ md5sum mitfi_config.txt
9c508e843d4e606ae66a0236c7cd5985  mitfi_config.txt
$ md5sum gc.prt
832f30603211c17f37a58faf9a05278b  gc.prt

[AlesBucek]

Md5sums are identical.

[linzhi2013]

Md5sums are identical.

That's weird.

I don't know what to do next...

Perhaps you should try Docker or Singularity version if possible.

[AlesBucek]

I'm now running MitoZ with Singularity without any problems. I did not try to resolve the java problem any further. Thanks for your help an suggestions.

[linzhi2013]

I'm now running MitoZ with Singularity without any problems. I did not try to resolve the java problem any further. Thanks for your help an suggestions.

You're welcome!

Please feel free to open new issues when you have questions.