Error with test data - STAR tmp

[laurie-tonon]

Hi,

I tried using the V3 version of SpliceLauncher but I can't make it run on my data and even on the test data files.

I launch the following command:

SpliceLauncher.sh --runMode Align,Count,SpliceLauncher -C config.cfg -t 10 -F ~/softs/SpliceLauncher/dataTest/fastq/ -O outsplice_tdata --Graphics --tmpDir tmp

The problem is linked with the STAR tpm files I think, as the pipeline aligns only the first sample and skip the others.
The error arrives later, on the Data formating part:

   Import matrix count...
   Remove junction with low coverage...
Error in apply(tmp[, c(6:ncol(tmp))], 1, max) :
  dim(X) must have a positive length
Execution halted

But I noticed this in the log file:

###### Alignment process ######
##### FASTQ files ######
-rw-r--r-- 1 tonon GRP_SYNC_GNOMIC 4.7M Apr  5  2022 A7BDE-785-01-07-111-0075_T.fastq.gz
-rw-r--r-- 1 tonon GRP_SYNC_GNOMIC 3.1M Apr  5  2022 A7BDE-785-02-07-111-0075_U.fastq.gz
-rw-r--r-- 1 tonon GRP_SYNC_GNOMIC 2.8M Apr  5  2022 A7BDE-785-03-07-111-0082_T.fastq.gz
-rw-r--r-- 1 tonon GRP_SYNC_GNOMIC 2.8M Apr  5  2022 A7BDE-785-04-07-111-0082_U.fastq.gz
-rw-r--r-- 1 tonon GRP_SYNC_GNOMIC 4.2M Apr  5  2022 A7BDE-785-05-07-111-0085_T.fastq.gz
treatment of A7BDE-785-01-07-111-0075_T.fastq.gz...
treatment of A7BDE-785-02-07-111-0075_U.fastq.gz...
treatment of A7BDE-785-03-07-111-0082_T.fastq.gz...
treatment of A7BDE-785-04-07-111-0082_U.fastq.gz...
treatment of A7BDE-785-05-07-111-0085_T.fastq.gz...
###### Make BAM index ######
-rw-r--r-- 1 tonon GRP_SYNC_GNOMIC 9.3M Mar 27 09:09 A7BDE-785-01-07-111-0075_T.Aligned.out.bam
treatment of A7BDE-785-01-07-111-0075_T.Aligned.out.bam...
[bam_sort_core] merging from 0 files and 10 in-memory blocks...
###### Finished! ######
###############################################
####### Launch counting step
###############################################

Only the first sample is aligned, leading to the error later where the script expect several columns in the dataframe and only got one.

It's confirmed by the STAR log files of the other samples:

EXITING because of fatal ERROR: could not make temporary directory: /home/tonon/sandbox/test_splicelauncher/test_pipe/tmp/
SOLUTION: (i) please check the path and writing permissions
 (ii) if you specified --outTmpDir, and this directory exists - please remove it before running STAR

Mar 27 09:09:33 ...... FATAL ERROR, exiting

I use STAR version 2.7.8a, the same one I used with the V2 version of SpliceLauncher.

How can I solve this to run the pipeline on my samples?

Thanks