Exception in thread "main" java.lang.NumberFormatException:

[Jokendo-collab]

I did run the rtandem successfully but when I am now running the perseGear I get the following error. What could be the problem?

parserGear(file = idfile, db = dbfile, decoyPrefix="#REV#",xmx=1,thread=4,outdir = "parser_outdir")
Exception in thread "main" java.lang.NumberFormatException: For input string: "PT5786.951S"
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at java.lang.Double.valueOf(Double.java:502)
at cn.bgi.MainRun.run(MainRun.java:317)
at cn.bgi.MainRun.main(MainRun.java:58)
Warning message:
In system(command = tandemparser, intern = TRUE) :
running command '/opt/exp_soft/miniconda3/bin/java -Xmx1G -jar "/home/oknjav001/R/x86_64-pc-linux-gnu-library/3.6/PGA/parser4PGA.jar" ".//180731_C0_CH_T016BCG.mzML_xtandem.xml" "/scratch/oknjav001/transcriptomics/proteogenomics/dbcreation/customdb/T042PPD_merge-var.fasta" "pga" "parser_outdir" "#REV#" "VAR" 1 4' had status 1

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so

locale:
[1] LC_CTYPE=en_ZA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_ZA.UTF-8 LC_COLLATE=en_ZA.UTF-8
[5] LC_MONETARY=en_ZA.UTF-8 LC_MESSAGES=en_ZA.UTF-8
[7] LC_PAPER=en_ZA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_ZA.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] PGA_1.16.0 rTANDEM_1.26.0 Rcpp_1.0.1
[4] XML_3.99-0.3 data.table_1.12.8 Biostrings_2.54.0
[7] XVector_0.26.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[10] IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0

loaded via a namespace (and not attached):
[1] Biobase_2.46.0 httr_1.4.1
[3] bit64_0.9-7 assertthat_0.2.1
[5] askpass_1.1 BiocFileCache_1.10.2
[7] blob_1.2.1 BSgenome_1.54.0
[9] GenomeInfoDbData_1.2.2 Rsamtools_2.2.3
[11] progress_1.2.2 pillar_1.4.4
[13] RSQLite_2.2.0 lattice_0.20-38
[15] glue_1.3.1 digest_0.6.25
[17] RColorBrewer_1.1-2 colorspace_1.4-1
[19] Matrix_1.2-17 plyr_1.8.6
[21] pkgconfig_2.0.3 pheatmap_1.0.12
[23] customProDB_1.26.1 biomaRt_2.42.1
[25] zlibbioc_1.32.0 purrr_0.3.4
[27] scales_1.1.0 processx_3.4.2
[29] BiocParallel_1.20.1 tibble_3.0.1
[31] openssl_1.4.1 ggplot2_3.3.0
[33] AhoCorasickTrie_0.1.0 ellipsis_0.3.0
[35] SummarizedExperiment_1.16.1 GenomicFeatures_1.38.2
[37] magrittr_1.5 crayon_1.3.4
[39] memoise_1.1.0 ps_1.3.2
[41] MASS_7.3-51.4 tools_3.6.0
[43] prettyunits_1.1.1 hms_0.5.3
[45] lifecycle_0.2.0 matrixStats_0.56.0
[47] stringr_1.4.0 munsell_0.5.0
[49] DelayedArray_0.12.3 AnnotationDbi_1.48.0
[51] ade4_1.7-15 compiler_3.6.0
[53] rlang_0.4.6 grid_3.6.0
[55] RCurl_1.98-1.2 VariantAnnotation_1.32.0
[57] rappdirs_0.3.1 bitops_1.0-6
[59] gtable_0.3.0 DBI_1.1.0
[61] curl_4.3 R6_2.4.1
[63] GenomicAlignments_1.22.1 Nozzle.R1_1.1-1
[65] dplyr_0.8.5 rtracklayer_1.46.0
[67] seqinr_3.6-1 bit_1.1-15.2
[69] readr_1.3.1 stringi_1.4.3
[71] vctrs_0.2.4 dbplyr_1.4.3
[73] tidyselect_1.0.0

[wenbostar]

Hi Javan，
Could you please try to use MGF format MS/MS data not mzML for peptide identification? This may be the reason that your mzML is not compatible with R version X!Tandem.
Bo