husonlab / malt Goto Github PK

When running MALT version 0.4.1 (built 24 May 2018), and I try to export the alignments in SAM format, I get the following error when using either --format or -f

jloda.util.UsageException: Invalid, unknown or duplicate option: --format
, use option '-h' for help
        at jloda.util.ArgsOptions.done(ArgsOptions.java:210)
        at malt.MaltRun.run(MaltRun.java:215)
        at malt.MaltRun.main(MaltRun.java:75)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:65)
        at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:57)

Example command:

malt-run -J-Xmx32g -t 8 -v -o . -d mini-database/ -id 85 -m BlastN -at SemiGlobal -top 1 -supp 0.01 -mq 100 --memoryMode load -i fastqs/* -ssc -sps --format

Hello,

I hope you can help me, I've tried all day to get MALT running and import files to MEGAN.

Always get the note
/home/xxx/SCRATCH_NOBAK/16S/BatMix_F1_new.fasta', skipped (java.io.IOException: Unknown file error (perhaps invalid file format?))

Though there is always a file produced (without any suffix)

Here is my input:
./malt-run --mode BlastN --inFile ~/SCRATCH/16S/new.fasta --index ~/SCRATCH/db/silva16s --output ~/SCRATCH/16S/output_malt7 --alignmentType SemiGlobal

The output file from MALT is not readable by MEGAN, would I need to convrt it first? Its also not a SAM file....

Thanks for your help
Best,
Claudia

I'm a member of the Debian Med team which is a group inside Debian with the objective to package free software in life sciences and medicine for official Debian. I intend to package malt. To let us know what you consider stable code ready for distribution it would help if you would consider tagging releases with versions. This would enable us to use automatic detection of new releases and we can guarantee to always distribute the latest and greates code.
Thanks for considering, Andreas.

Hi,
I have a error when I execute in non-gui console mode.

I installed MALT with the follow command.

./MALT_unix 0.5.3.sh -c

Could you help me?

Thanks in advance

Hi,

I used the following command to build the index for my databases:

malt-build -i h_abfpv_genome.fasta -s DNA -d h_abfpv_genome -t 10 -a2taxonomy nucl_acc2tax-Oct2017.abin

(The default the maximum memory usage is 64G)
But it exit for the error as below:

Version MALT (version 0.4.0, built 6 Sep 2017)
Copyright (C) 2017 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Reference sequence type set to: DNA
Seed shape(s): 111110111011110110111111
Reading file: h_abfpv_genome.fasta
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (3064.9s)
Number of sequences: 317085
Number of letters: 47386139371
BUILDING table (0)...
Number of seeds in references: 47378846416
TableSize= 2147483639
hashMask.length= 31
maxHitsPerHash set to: 1000
Initializing arrays...
100% (0.0s)
Java HotSpot(TM) 64-Bit Server VM warning: INFO: os::commit_memory(0x00002b9694080000, 17179869184, 0) failed; error='Cannot allocate memory' (errno=12)

I tried to adjust the maximum memory usage to 128G, But it doesn't work...Can anyone help me ?

Thanks very much!
Best wishes,
Myshu

I am using MALT (version 0.4.1, built 24 May 2018) to align my DNA reads to a reference database. I got this warning n some of my jobs.

Nov 16, 2018 11:53:59 AM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.

Resulting rma6 files seems normal but do you have any idea about the problem?