Exception in thread "main" java.lang.NumberFormatException #82
Description
Hi, i am trying to use java -jar PDV-2.1.0.jar to export some of the my spectrums, i tested psm.tsv and pep.xml for rt input and calibrated.mzML for st input like this
rt_1=../CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/psm.tsv rt_2=../CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2_52_1_3562_d/interact-CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.pep.xml and st_2=../CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562_calibrated.mzML
both of them came from the output of fragpipe, and my raw file format is .d, which is bruker tdf file.
I used the following commands and they both failed, can you help me to fix this? Thank you!
Exception in thread "main" java.lang.NumberFormatException: For input string: "CAD20241022licq_BSEP_PreExp_DDA_60min_F2_Slot2-52_1_3562.00083.00083.4"
java -jar PDV-2.1.0.jar -r $rt_1 -rt 4 -s $st_2 -st 2 -i ../spectrum_scan_number.txt -k s -o output_F2 -a 0.05 -c 3 -pw 1 -fw 800 -fh 400 -fu px -ft pdf
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
java -jar PDV-2.1.0.jar -r $rt_2 -rt 2 -s $st_2 -st 2 -i ../spectrum_scan_number.txt -k s -o output_F2 -a 0.05 -c 3 -pw 1 -fw 800 -fh 400 -fu px -ft pdf
../spectrum_scan_number.txt contains only a single number.