Problem running the nextflow script

[KarlKaise]

Hello,

Upon running the nextflox script I came across this issue.

I would be grateful for any help. Thank you.

bash flop_launcher.sh -t
** Resuming transfer from byte position 1010108
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Archive: test_data.zip
##TEST MODE##
Nextflow 24.04.2 is available - Please consider updating your version to it
N E X T F L O W ~ version 23.10.1
Launching flop.nf [high_yalow] DSL2 - revision: 220854d6d5
##########################################################################
Welcome to
.------..------..------..------.
|F.--. ||L.--. ||O.--. ||P.--. |
| :(): || :/: || :/: || :/: |
| ()() || () || :/: || () |
| -- F|| -- L|| -- O|| -- P|
'------''------''------''------'

The FunctionaL Omics Preprocessing platform is
a workflow meant to evaluate the impact of different
normalization and differential expression tools on the
resulting functional space, in the context of bulk RNA-seq data.

##########################################################################
executor > local (2)
executor > local (2)
[- ] process > get_prsources -
[45/6d2f44] process > contrast_creator (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > diffexp_analysis -
[- ] process > output_merge_de -
[- ] process > downstream_merge_de -
[- ] process > func_decoupler -
[- ] process > decoupler_merger -
[- ] process > subset_merger -
[- ] process > rank_analysis -
[- ] process > top_bottom_overlap_analysis -
ERROR ~ Error executing process > 'contrast_creator (1)'
Caused by:
Process contrast_creator (1) terminated with an error exit status (139)
Command executed:
Rscript flop/scripts/contrast_creator.R --file_dir test
Command exit status:
139
Command output:
(empty)
Command error:
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.4 ✔ readr 2.1.5
✔ forcats 1.0.0 ✔ stringr 1.5.1
✔ ggplot2 3.5.1 ✔ tibble 3.2.1
✔ lubridate 1.9.3 ✔ tidyr 1.3.1
✔ purrr 1.0.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (http://conflicted.r-lib.org/) to force all conflicts to become errors
qs 0.25.5
Rows: 24961 Columns: 67
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (1): gene_symbol
dbl (66): ASPC_DMSO__24, ASPC_DMSO__24.1, ASPC_DMSO__24.2, ASPC_DMSO__24.3, ...

ℹ Use spec() to retrieve the full column specification for this data.
ℹ Specify the column types or set show_col_types = FALSE to quiet this message.
Rows: 66 Columns: 2
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (2): sample_ID, group

ℹ Use spec() to retrieve the full column specification for this data.
ℹ Specify the column types or set show_col_types = FALSE to quiet this message.
Rows: 3 Columns: 2
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (2): group1, group2

ℹ Use spec() to retrieve the full column specification for this data.
ℹ Specify the column types or set show_col_types = FALSE to quiet this message.

*** caught segfault ***
address 0x19, cause 'memory not mapped'

Traceback:
1: qsave(sel_metadata, meta_name)
An irrecoverable exception occurred. R is aborting now ...
.command.sh: line 2: 2751013 Segmentation fault (core dumped) Rscript flop/scripts/contrast_creator.R --file_dir test
Work dir:
/flop/work/45/6d2f447b5a22df86c8cd1323fc0018
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
-- Check '.nextflow.log' file for details
WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info.