RE: metatrans pipeline error

[Magdy S Alabady]

Hello,

 

I run into an error while running the “metatrans pipeline”. The log files don’t tell me much. Here is the error:

 

 

Error in fnumTofcol[1, j] : subscript out of bounds

Execution halted

 

 

The file processing modules seem to be completed successfully and this error appears to be associated with the differential analysis part. Here is my metadata file:

 

#SampleName        SampleFiles  Shortname   Order Type   Description  F1_InfluxStrict            F2_Influx

LOOE_07_12           LOOE_07_12_R1.fastq.gz,LOOE_07_12_R2.fastq.gz           LOOE_07_12            1          mrna  LOOE_07_12           NODUST       DUST

LOOE_07_13           LOOE_07_13_R1.fastq.gz,LOOE_07_13_R2.fastq.gz           LOOE_07_13            2          mrna  LOOE_07_13           NODUST       DUST

LOOE_07_14           LOOE_07_14_R1.fastq.gz,LOOE_07_14_R2.fastq.gz           LOOE_07_14            3          mrna  LOOE_07_14           NODUST       NODUST

LOOE_07_15           LOOE_07_15_R1.fastq.gz,LOOE_07_15_R2.fastq.gz           LOOE_07_15            4          mrna  LOOE_07_15           NODUST       NODUST

LOOE_07_16           LOOE_07_16_R1.fastq.gz,LOOE_07_16_R2.fastq.gz           LOOE_07_16            5          mrna  LOOE_07_16           NODUST       NODUST

LOOE_07_20           LOOE_07_20_R1.fastq.gz,LOOE_07_20_R2.fastq.gz           LOOE_07_20            6          mrna  LOOE_07_20           NODUST       NODUST

LOOE_07_22           LOOE_07_22_R1.fastq.gz,LOOE_07_22_R2.fastq.gz           LOOE_07_22            7          mrna  LOOE_07_22           NODUST       NODUST

LOOE_07_23           LOOE_07_23_R1.fastq.gz,LOOE_07_23_R2.fastq.gz           LOOE_07_23            8          mrna  LOOE_07_23           NODUST       NODUST

LOOE_07_24           LOOE_07_24_R1.fastq.gz,LOOE_07_24_R2.fastq.gz           LOOE_07_24            9          mrna  LOOE_07_24           NODUST       NODUST

LOOE_07_25           LOOE_07_25_R1.fastq.gz,LOOE_07_25_R2.fastq.gz           LOOE_07_25            10       mrna  LOOE_07_25           NODUST       DUST

LOOE_07_26           LOOE_07_26_R1.fastq.gz,LOOE_07_26_R2.fastq.gz           LOOE_07_26            11       mrna  LOOE_07_26           NODUST       DUST

LOOE_07_27           LOOE_07_27_R1.fastq.gz,LOOE_07_27_R2.fastq.gz           LOOE_07_27            12       mrna  LOOE_07_27           NODUST       NODUST

LOOE_07_28           LOOE_07_28_R1.fastq.gz,LOOE_07_28_R2.fastq.gz           LOOE_07_28            13       mrna  LOOE_07_28           DUST  DUST

LOOE_07_29           LOOE_07_29_R1.fastq.gz,LOOE_07_29_R2.fastq.gz           LOOE_07_29            14       mrna  LOOE_07_29           DUST  DUST

LOOE_07_30           LOOE_07_30_R1.fastq.gz,LOOE_07_30_R2.fastq.gz           LOOE_07_30            15       mrna  LOOE_07_30           NODUST       NODUST

LOOE_07_31           LOOE_07_31_R1.fastq.gz,LOOE_07_31_R2.fastq.gz           LOOE_07_31            16       mrna  LOOE_07_31           DUST  DUST

LOOE_08_01           LOOE_08_01_R1.fastq.gz,LOOE_08_01_R2.fastq.gz           LOOE_08_01            17       mrna  LOOE_08_01           NODUST       DUST

LOOE_08_03           LOOE_08_03_R1.fastq.gz,LOOE_08_03_R2.fastq.gz           LOOE_08_03            18       mrna  LOOE_08_03           DUST  DUST

LOOE_08_04           LOOE_08_04_R1.fastq.gz,LOOE_08_04_R2.fastq.gz           LOOE_08_04            19       mrna  LOOE_08_04           NODUST       DUST

LOOE_08_05           LOOE_08_05_R1.fastq.gz,LOOE_08_05_R2.fastq.gz           LOOE_08_05            20       mrna  LOOE_08_05           NODUST       NODUST

LOOE_08_06           LOOE_08_06_R1.fastq.gz,LOOE_08_06_R2.fastq.gz           LOOE_08_06            21       mrna  LOOE_08_06           NODUST       NODUST

 

 

I also, changes F2_influx to “F0_influx” to excluded this factor, but I still got the same error.

 

 

Anny suggestions?

 

Thanks,

Magdy

 

__________________________________________________________

Magdy S. Alabady, Ph.D.

Associate Research Scientist | Plant Biology Department | 706 542-6503

Director | Georgia Genomics and Bioinformatics Core Lab | 706 542-6877

University of Georgia, Athens, GA 30602, USA

 

[metatr...@gmail.com]

Hi Magdy,

Not sure if this is related to your error, but try to use "dash" instead of "underscore" in the factor column names, e.g. F0-influx (as described here: http://metatrans.org/#metadata).

Could you check if your Python version is 2.7.3?

However, the error might come from many sources, first thing to check would be to run the test, following the instruction in the README.txt file from the website pointed above.

If that test works, then you could check your samples work in a tested environment, i.e. a computer or a virtual box with an Ubuntu 14.04 image. The versions that were used

when developing the pipeline are described in "-Programming languages that were used:".

Sorry we haven't had the opportunity to test the pipeline in higher versions of the software used, so we cannot provide so much support for now.

Hope this helps