SAGE error in Big dataset TMT

### Description of the bug

```
ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:TMT:ID:PSMRESCORING:PERCOLATOR (g00594_Prot_37_11)'

Caused by:
Process `NFCORE_QUANTMS:QUANTMS:TMT:ID:PSMRESCORING:PERCOLATOR (g00594_Prot_37_11)` terminated with an error exit status (9)

Command executed:

OMP_NUM_THREADS=48 PercolatorAdapter \
-in g00594_Prot_37_11_sage.idXML \
-out g00594_Prot_37_11_sage_perc.idXML \
-threads 48 \
-subset_max_train 300000 \
-decoy_pattern DECOY_ \
-post_processing_tdc \
-score_type pep \
-debug 0 \
2>&1 | tee g00594_Prot_37_11_sage_percolator.log

cat <<-END_VERSIONS > versions.yml
"NFCORE_QUANTMS:QUANTMS:TMT:ID:PSMRESCORING:PERCOLATOR":
PercolatorAdapter: $(PercolatorAdapter 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
percolator: $(percolator -h 2>&1 | grep -E '^Percolator version(.*)' | sed 's/Percolator version //g')
END_VERSIONS

Command exit status:
9

Command output:
Loading input file: g00594_Prot_37_11_sage.idXML
Merging peptide ids.
Merging protein ids.
Prepared percolator input.
Standard output: Running: /usr/local/bin/percolator -U -m /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_target_pout_psms.tab -M /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_decoy_pout_psms.tab --num-threads 48 -N 300000 -Y /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_pin.tab

Standard error: Percolator version 3.05.0, Build Date Aug 31 2020 19:03:04
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
/usr/local/bin/percolator -U -m /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_target_pout_psms.tab -M /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_decoy_pout_psms.tab --num-threads 48 -N 300000 -Y /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_pin.tab
Started Sat Dec 9 15:05:43 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_pin.tab
Features:
mass peplen charge2 charge3 charge4 charge5 enzN enzC enzInt dm absdm score SAGE:ln(-poisson) SAGE:ln(delta_best) SAGE:ln(delta_next) SAGE:ln(matched_intensity_pct) SAGE:longest_b SAGE:longest_y SAGE:longest_y_pct SAGE:matched_peaks SAGE:scored_candidates
Found 33916 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 16926 positives and 16990 negatives, size ratio=0.996233 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1: Exception caught: Error in the input data: cannot find an initial direction with positive training examples. Consider setting/raising the initial training FDR threshold (--train-initial-fdr).
Terminating.

Process '/usr/local/bin/percolator' did not finish successfully (exit code: ). Please check the log.

PercolatorAdapter took 2.54 s (wall), 2.28 s (CPU), 0.08 s (system), 2.20 s (user); Peak Memory Usage: 168 MB.

Command wrapper:
Loading input file: g00594_Prot_37_11_sage.idXML
Merging peptide ids.
Merging protein ids.
Prepared percolator input.
Standard output: Running: /usr/local/bin/percolator -U -m /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_target_pout_psms.tab -M /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_decoy_pout_psms.tab --num-threads 48 -N 300000 -Y /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_pin.tab

Standard error: Percolator version 3.05.0, Build Date Aug 31 2020 19:03:04
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
/usr/local/bin/percolator -U -m /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_target_pout_psms.tab -M /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_decoy_pout_psms.tab --num-threads 48 -N 300000 -Y /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_pin.tab
Started Sat Dec 9 15:05:43 2023
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile /tmp/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_1/20231209_150541_hl-codon-bm-10.ebi.ac.uk_42_2_pin.tab
Features:
mass peplen charge2 charge3 charge4 charge5 enzN enzC enzInt dm absdm score SAGE:ln(-poisson) SAGE:ln(delta_best) SAGE:ln(delta_next) SAGE:ln(matched_intensity_pct) SAGE:longest_b SAGE:longest_y SAGE:longest_y_pct SAGE:matched_peaks SAGE:scored_candidates
Found 33916 PSMs
Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores.
Train/test set contains 16926 positives and 16990 negatives, size ratio=0.996233 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Split 1: Exception caught: Error in the input data: cannot find an initial direction with positive training examples. Consider setting/raising the initial training FDR threshold (--train-initial-fdr).
Terminating.

Process '/usr/local/bin/percolator' did not finish successfully (exit code: ). Please check the log.

PercolatorAdapter took 2.54 s (wall), 2.28 s (CPU), 0.08 s (system), 2.20 s (user); Peak Memory Usage: 168 MB.

Work dir:
/hps/nobackup/juan/pride/reanalysis/absolute-expression/cell-lines/MSV000085836/work/9a/8f8f857d333f8a6b2224af6bac7059

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

```

### Command used and terminal output

_No response_

### Relevant files

_No response_

### System information

_No response_