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taxonomicallyinformedannotation / tima-r

https://taxonomicallyinformedannotation.github.io/tima-r/
https://taxonomicallyinformedannotation.github.io/tima-r
GNU General Public License v3.0
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tima-r Error on ESI(-) #116

Closed anani-a-missinou closed 2 months ago

anani-a-missinou commented 5 months ago

Hi dear developers,

I ran my plant metabolomic data on the Sirius version (v5.8.5) and I would like to provide it to your tima-r GUI.

Now everything is executed correctly for ESI(+) files, however, I have another error with the ESI(-) files, for which TIMA stops immediately after the start. I always get this error:

(base) $ pwd /mnt/d/tools/computational_metabolomics/tima-r

MGF file

(base) $ more data/source/brassimet_leaves-roots_pacs_neg.mgf BEGIN IONS FEATURE_ID=315 PEPMASS=260.911 SCANS=315 RTINSECONDS=36.518 CHARGE=0- MSLEVEL=2 MERGED_STATS=1 / 4 (0 removed due to low quality, 3 removed due to low cosine). 96.971 2.3E2 97.029 2.1E2 116.006 9.0E1 144.015 1.3E2 152.915 1.3E2 196.903 4.3E2 197.912 2.0E2 215.923 2.0E2 242.901 1.9E2 END IONS

BEGIN IONS FEATURE_ID=3246 PEPMASS=261.127 SCANS=3246 RTINSECONDS=420.041 CHARGE=0- MSLEVEL=2 MERGED_STATS=2 / 2 (0 removed due to low quality, 0 removed due to low cosine). 114.056 6.1E3 114.673 9.2E1 115.059 3.4E2 172.008 8.0E1 219.737 8.0E1 221.841 1.1E2 222.839 9.2E1 223.840 1.2E2 END IONS

BEGIN IONS FEATURE_ID=391 PEPMASS=262.057 SCANS=391 RTINSECONDS=40.4 CHARGE=0- MSLEVEL=2 MERGED_STATS=1 / 5 (1 removed due to low quality, 3 removed due to low cosine). 96.008 1.3E2 96.041 2.0E2 96.958 2.7E2 97.029 2.2E2 97.146 8.0E1 111.043 1.3E2 115.005 8.8E1 129.019 1.1E2 133.015 2.6E2 198.901 9.2E1 198.924 1.0E2 244.911 9.2E1 260.011 8.2E1 END IONS

quant CSV

(base) $ more data/source/brassimet_leaves-roots_pacs_neg.csv row ID,row m/z,row retention time,Leaves_s105_neg.mzXML Peak area,Leaves_s107_neg.mzXML Peak area,Leaves_s106_neg.mzXML Peak area,Leaves_s108_neg.mzXML Peak area,Leaves_s104_neg.mzXML Peak area,Leaves_s100_neg.m zXML Peak area,Leaves_s110_neg.mzXML Peak area,Leaves_s103_neg.mzXML Peak area,Leaves_s102_neg.mzXML Peak area,Leaves_s10_neg.mzXML Peak area,Leaves_s101_neg.mzXML Peak area,Leaves_s109_neg.mzXML Peak area,Leave s_s11_neg.mzXML Peak area,Leaves_s12_neg.mzXML Peak area,Leaves_s112_neg.mzXML Peak area,Leaves_s111_neg.mzXML Peak area,Leaves_s16_neg.mzXML Peak area,Leaves_s113_neg.mzXML Peak area,Leaves_s13_neg.mzXML Peak a rea,Leaves_s115_neg.mzXML Peak area,Leaves_s15_neg.mzXML Peak area,Leaves_s14_neg.mzXML Peak area,Leaves_s114_neg.mzXML Peak area,Leaves_s116_neg.mzXML Peak area,Leaves_s3_neg.mzXML Peak area,Leaves_s19_neg.mzXM L Peak area,Leaves_s1_neg.mzXML Peak area,Leaves_s22_neg.mzXML Peak area,Leaves_s21_neg.mzXML Peak area,Leaves_s4_neg.mzXML Peak area,Leaves_s48_neg.mzXML Peak area,Leaves_s17_neg.mzXML Peak area,Leaves_s20_neg. mzXML Peak area,Leaves_s18_neg.mzXML Peak area,Leaves_s49_neg.mzXML Peak area,Leaves_s2_neg.mzXML Peak area,Leaves_s53_neg.mzXML Peak area,Leaves_s58_neg.mzXML Peak area,Leaves_s54_neg.mzXML Peak area,Leaves_s57 _neg.mzXML Peak area,Leaves_s55_neg.mzXML Peak area,Leaves_s50_neg.mzXML Peak area,Leaves_s61_neg.mzXML Peak area,Leaves_s59_neg.mzXML Peak area,Leaves_s60_neg.mzXML Peak area,Leaves_s51_neg.mzXML Peak area,Leav es_s56_neg.mzXML Peak area,Leaves_s67_neg.mzXML Peak area,Leaves_s6_neg.mzXML Peak area,Leaves_s69_neg.mzXML Peak area,Leaves_s63_neg.mzXML Peak area,Leaves_s65_neg.mzXML Peak area,Leaves_s64_neg.mzXML Peak area ,Leaves_s95_neg.mzXML Peak area,Leaves_s66_neg.mzXML Peak area,Leaves_s5_neg.mzXML Peak area,Leaves_s52_neg.mzXML Peak area,Leaves_s68_neg.mzXML Peak area,Roots_s151_neg.mzXML Peak area,Roots_s143_neg.mzXML Peak area,Roots_s148_neg.mzXML Peak area,Roots_s153_neg.mzXML Peak area,Roots_s144_neg.mzXML Peak area,Leaves_s8_neg.mzXML Peak area,Leaves_s99_neg.mzXML Peak area,Leaves_s97_neg.mzXML Peak area,Leaves_s62_neg.mzXML Peak area,Leaves_s7_neg.mzXML Peak area,Roots_s152_neg.mzXML Peak area,Roots_s155_neg.mzXML Peak area,Roots_s149_neg.mzXML Peak area,Roots_s154_neg.mzXML Peak area,Leaves_s98_neg.mzXML Peak area,Leaves_s9_neg.m zXML Peak area,Roots_s158_neg.mzXML Peak area,Leaves_s96_neg.mzXML Peak area,Roots_s145_neg.mzXML Peak area,Roots_s150_neg.mzXML Peak area,Roots_s146_neg.mzXML Peak area,Roots_s147_neg.mzXML Peak area,Roots_s159 _neg.mzXML Peak area,Roots_s163_neg.mzXML Peak area,Roots_s191_neg.mzXML Peak area,Roots_s164_neg.mzXML Peak area,Roots_s190_neg.mzXML Peak area,Roots_s157_neg.mzXML Peak area,Roots_s160_neg.mzXML Peak area,Root s_s200_neg.mzXML Peak area,Roots_s156_neg.mzXML Peak area,Roots_s195_neg.mzXML Peak area,Roots_s192_neg.mzXML Peak area,Roots_s199_neg.mzXML Peak area,Roots_s239_neg.mzXML Peak area,Roots_s193_neg.mzXML Peak are a,Roots_s201_neg.mzXML Peak area,Roots_s198_neg.mzXML Peak area,Roots_s205_neg.mzXML Peak area,Roots_s206_neg.mzXML Peak area,Roots_s203_neg.mzXML Peak area,Roots_s197_neg.mzXML Peak area,Roots_s194_neg.mzXML Pe ak area,Roots_s204_neg.mzXML Peak area,Roots_s202_neg.mzXML Peak area,Roots_s246_neg.mzXML Peak area,Roots_s240_neg.mzXML Peak area,Roots_s208_neg.mzXML Peak area,Roots_s241_neg.mzXML Peak area,Roots_s235_neg.mz XML Peak area,Roots_s234_neg.mzXML Peak area,Roots_s237_neg.mzXML Peak area,Roots_s238_neg.mzXML Peak area,Roots_s207_neg.mzXML Peak area,Roots_s209_neg.mzXML Peak area,Roots_s196_neg.mzXML Peak area,Rootss249 neg.mzXML Peak area,Roots_s248_neg.mzXML Peak area,Roots_s255_neg.mzXML Peak area,Roots_s242_neg.mzXML Peak area,Roots_s254_neg.mzXML Peak area,Roots_s244_neg.mzXML Peak area,Roots_s236_neg.mzXML Peak area,Roots _s243_neg.mzXML Peak area,Roots_s253_neg.mzXML Peak area,Roots_s247_neg.mzXML Peak area,Roots_s250_neg.mzXML Peak area,Roots_s252_neg.mzXML Peak area,Roots_s251_neg.mzXML Peak area,Roots_s245_neg.mzXML Peak area

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taxonomic metadata

(base) $ more data/source/brassimet_leaves-roots-neg_pacs_taxonomic_metadata_v2.tsv filename ATTRIBUTE_species Leaves_s115_neg.mzXML Brassica oleracea Leaves_s21_neg.mzXML Brassica oleracea Leaves_s68_neg.mzXML Brassica oleracea Leaves_s105_neg.mzXML Brassica oleracea Leaves_s11_neg.mzXML Brassica oleracea Leaves_s58_neg.mzXML Brassica oleracea Leaves_s106_neg.mzXML Brassica oleracea Leaves_s12_neg.mzXML Brassica oleracea Leaves_s59_neg.mzXML Brassica oleracea Leaves_s107_neg.mzXML Brassica oleracea Leaves_s13_neg.mzXML Brassica oleracea Leaves_s60_neg.mzXML Brassica oleracea Leaves_s108_neg.mzXML Brassica oleracea Leaves_s14_neg.mzXML Brassica oleracea Leaves_s61_neg.mzXML Brassica oleracea Leaves_s109_neg.mzXML Brassica oleracea Leaves_s15_neg.mzXML Brassica oleracea Leaves_s62_neg.mzXML Brassica oleracea Leaves_s110_neg.mzXML Brassica oleracea Leaves_s16_neg.mzXML Brassica oleracea Leaves_s63_neg.mzXML Brassica oleracea Leaves_s111_neg.mzXML Brassica oleracea Leaves_s17_neg.mzXML Brassica oleracea Leaves_s64_neg.mzXML Brassica oleracea Leaves_s112_neg.mzXML Brassica oleracea Leaves_s18_neg.mzXML Brassica oleracea Leaves_s65_neg.mzXML Brassica oleracea Leaves_s113_neg.mzXML Brassica oleracea Leaves_s19_neg.mzXML Brassica oleracea Leaves_s66_neg.mzXML Brassica oleracea Leaves_s114_neg.mzXML Brassica oleracea Leaves_s20_neg.mzXML Brassica oleracea Leaves_s67_neg.mzXML Brassica oleracea Leaves_s116_neg.mzXML Brassica rapa Leaves_s22_neg.mzXML Brassica rapa Leaves_s69_neg.mzXML Brassica rapa Leaves_s1_neg.mzXML Brassica rapa Leaves_s48_neg.mzXML Brassica rapa Leaves_s95_neg.mzXML Brassica rapa Leaves_s2_neg.mzXML Brassica rapa Leaves_s49_neg.mzXML Brassica rapa Leaves_s96_neg.mzXML Brassica rapa Leaves_s3_neg.mzXML Brassica rapa Leaves_s50_neg.mzXML Brassica rapa Leaves_s97_neg.mzXML Brassica rapa Leaves_s4_neg.mzXML Brassica rapa Leaves_s51_neg.mzXML Brassica rapa Leaves_s98_neg.mzXML Brassica rapa Leaves_s5_neg.mzXML Brassica rapa Leaves_s52_neg.mzXML Brassica rapa Leaves_s99_neg.mzXML Brassica rapa Leaves_s100_neg.mzXML Brassica rapa Leaves_s53_neg.mzXML Brassica rapa Leaves_s6_neg.mzXML Brassica rapa Leaves_s101_neg.mzXML Brassica rapa Leaves_s54_neg.mzXML Brassica rapa Leaves_s7_neg.mzXML Brassica rapa Leaves_s102_neg.mzXML Brassica rapa Leaves_s55_neg.mzXML Brassica rapa Leaves_s8_neg.mzXML Brassica rapa Leaves_s103_neg.mzXML Brassica rapa Leaves_s56_neg.mzXML Brassica rapa Leaves_s9_neg.mzXML Brassica rapa Leaves_s10_neg.mzXML Brassica rapa Leaves_s104_neg.mzXML Brassica rapa Leaves_s57_neg.mzXML Brassica rapa Roots_s163_neg.mzXML Brassica oleracea Roots_s208_neg.mzXML Brassica oleracea Roots_s254_neg.mzXML Brassica oleracea Roots_s153_neg.mzXML Brassica oleracea Roots_s200_neg.mzXML Brassica oleracea Roots_s244_neg.mzXML Brassica oleracea Roots_s154_neg.mzXML Brassica oleracea Roots_s201_neg.mzXML Brassica oleracea Roots_s245_neg.mzXML Brassica oleracea Roots_s155_neg.mzXML Brassica oleracea Roots_s246_neg.mzXML Brassica oleracea Roots_s156_neg.mzXML Brassica oleracea Roots_s202_neg.mzXML Brassica oleracea Roots_s247_neg.mzXML Brassica oleracea Roots_s157_neg.mzXML Brassica oleracea Roots_s203_neg.mzXML Brassica oleracea Roots_s248_neg.mzXML Brassica oleracea Roots_s158_neg.mzXML Brassica oleracea Roots_s204_neg.mzXML Brassica oleracea Roots_s249_neg.mzXML Brassica oleracea Roots_s159_neg.mzXML Brassica oleracea Roots_s205_neg.mzXML Brassica oleracea Roots_s250_neg.mzXML Brassica oleracea Roots_s160_neg.mzXML Brassica oleracea Roots_s206_neg.mzXML Brassica oleracea Roots_s251_neg.mzXML Brassica oleracea Roots_s207_neg.mzXML Brassica oleracea Roots_s252_neg.mzXML Brassica oleracea Roots_s253_neg.mzXML Brassica oleracea Roots_s164_neg.mzXML Brassica rapa Roots_s209_neg.mzXML Brassica rapa Roots_s255_neg.mzXML Brassica rapa Roots_s143_neg.mzXML Brassica rapa Roots_s190_neg.mzXML Brassica rapa Roots_s234_neg.mzXML Brassica rapa Roots_s144_neg.mzXML Brassica rapa Roots_s191_neg.mzXML Brassica rapa Roots_s235_neg.mzXML Brassica rapa Roots_s145_neg.mzXML Brassica rapa Roots_s192_neg.mzXML Brassica rapa Roots_s236_neg.mzXML Brassica rapa Roots_s146_neg.mzXML Brassica rapa Roots_s193_neg.mzXML Brassica rapa Roots_s237_neg.mzXML Brassica rapa Roots_s147_neg.mzXML Brassica rapa Roots_s194_neg.mzXML Brassica rapa Roots_s238_neg.mzXML Brassica rapa Roots_s148_neg.mzXML Brassica rapa Roots_s195_neg.mzXML Brassica rapa Roots_s239_neg.mzXML Brassica rapa Roots_s149_neg.mzXML Brassica rapa Roots_s196_neg.mzXML Brassica rapa Roots_s240_neg.mzXML Brassica rapa Roots_s150_neg.mzXML Brassica rapa Roots_s197_neg.mzXML Brassica rapa Roots_s241_neg.mzXML Brassica rapa Roots_s151_neg.mzXML Brassica rapa Roots_s198_neg.mzXML Brassica rapa Roots_s242_neg.mzXML Brassica rapa Roots_s152_neg.mzXML Brassica rapa Roots_s199_neg.mzXML Brassica rapa Roots_s243_neg.mzXML Brassica rapa

Error after running of tima-r

tima-gui-1 | 2024-01-17 06:36:00.102067 Changing filenames tima-gui-1 | 2024-01-17 06:36:00.102297 Exporting params ... tima-gui-1 | ● completed target par_usr_pre_lib_sop_hmd [0.199 seconds] tima-gui-1 | ▶ dispatched target par_usr_pre_lib_sop_clo tima-gui-1 | 2024-01-17 06:36:00.317971 Loading default params tima-gui-1 | 2024-01-17 06:36:00.514703 All params tima-gui-1 | 2024-01-17 06:36:00.515034 Small params tima-gui-1 | 2024-01-17 06:36:00.515138 Changing params tima-gui-1 | 2024-01-17 06:36:00.515222 Changing filenames tima-gui-1 | 2024-01-17 06:36:00.51538 Exporting params ... tima-gui-1 | ● completed target par_usr_pre_lib_sop_clo [0.205 seconds] tima-gui-1 | ▶ dispatched target par_usr_cre_edg_spe tima-gui-1 | 2024-01-17 06:36:00.75158 Loading default params tima-gui-1 | 2024-01-17 06:36:00.931716 All params tima-gui-1 | 2024-01-17 06:36:00.932072 Small params tima-gui-1 | 2024-01-17 06:36:00.932204 Changing params tima-gui-1 | 2024-01-17 06:36:00.93233 Changing filenames tima-gui-1 | 2024-01-17 06:36:01.004152 Exporting params ... tima-gui-1 | ● completed target par_usr_cre_edg_spe [0.283 seconds] tima-gui-1 | ▶ dispatched target par_usr_pre_lib_sop_lot tima-gui-1 | 2024-01-17 06:36:01.21768 Loading default params tima-gui-1 | 2024-01-17 06:36:01.41915 All params tima-gui-1 | 2024-01-17 06:36:01.419487 Small params tima-gui-1 | 2024-01-17 06:36:01.419584 Changing params tima-gui-1 | 2024-01-17 06:36:01.41967 Changing filenames tima-gui-1 | 2024-01-17 06:36:01.419845 Exporting params ... tima-gui-1 | ● completed target par_usr_pre_lib_sop_lot [0.209 seconds] tima-gui-1 | ▶ dispatched target par_wei_ann tima-gui-1 | ● completed target par_wei_ann [0.018 seconds] tima-gui-1 | ▶ dispatched target par_ann_spe tima-gui-1 | ● completed target par_ann_spe [0.038 seconds] tima-gui-1 | ▶ dispatched target par_ann_mas tima-gui-1 | ● completed target par_ann_mas [0.02 seconds] tima-gui-1 | ▶ dispatched target par_cre_edg_spe tima-gui-1 | ● completed target par_cre_edg_spe [0.016 seconds] tima-gui-1 | ▶ dispatched target input_spectra tima-gui-1 | ● completed target input_spectra [0 seconds] tima-gui-1 | ▶ dispatched target fea_edg_spe tima-gui-1 | 2024-01-17 06:36:04.996394 Loading spectra... tima-gui-1 | ✖ errored target fea_edg_spe tima-gui-1 | ✖ errored pipeline [52.935 seconds] tima-gui-1 | Warning: Error in : Error running targets::tar_make() tima-gui-1 | Error messages: targets::tar_meta(fields = error, complete_only = TRUE) tima-gui-1 | Debugging guide: https://books.ropensci.org/targets/debugging.html tima-gui-1 | How to ask for help: https://books.ropensci.org/targets/help.html tima-gui-1 | Last error message: tima-gui-1 | error in evaluating the argument 'object' in selecting a method for function 'filterMsLevel': error in evaluating the argument 'object' in selecting a method for function 'Spectra': NA/NaN argument tima-gui-1 | Last error traceback: tima-gui-1 | create_edges_spectra(input = input_spectra, output = par_cre_edg_spe$fil... tima-gui-1 | import_spectra(input) tima-gui-1 | Spectra::filterMsLevel(Spectra::Spectra(MsBackendMgf::readMgf(f = file))... tima-gui-1 | Spectra::Spectra(MsBackendMgf::readMgf(f = file)) tima-gui-1 | MsBackendMgf::readMgf(f = file) tima-gui-1 | .extract_mgf_spectrum(mgf[begin[i]:end[i]], mapping = mapping) tima-gui-1 | grep("=", mgf) tima-gui-1 | is.factor(x) tima-gui-1 | .handleSimpleError(function (cond) .Internal(C_tryCatchHelper(addr, 1L,... tima-gui-1 | h(simpleError(msg, call)) tima-gui-1 | .handleSimple [... truncated] tima-gui-1 | 1: shiny::runApp tima-gui-1 exited with code 0

I can share my data in private. Thank you for your help

Adafede commented 5 months ago

Hi again @anani-a-missinou and thank you for opening this issue. With the first 3 lines, it looks like I can run the step without issue. Could you send me the full data? (rutz @ imsb.biol.ethz.ch)

Adafede commented 5 months ago

Thank you for sharing @anani-a-missinou, it looks like on line 88174 from your MGF (very end) there is an empty BEGIN IONS breaking things. Removing it solved the issue on my side.

Adafede commented 4 months ago

@anani-a-missinou Any update?

Adafede commented 2 months ago

I'll close for now.