Description
Hey everyone,
When I try to run percolator on my folder of pin files (which are themselves the output of comet runs), it seems like the execution is stuck on reading the first file:
$ percolator ./pin_files_PXD043200/*.pin -X ./output_files_PXD043200/comet_perc_PXD043200_out.xml
Protein decoy-prefix used is DECOY_
Reading file: ./pin_files_PXD043200/WEC14392X002__S79_IGF_d1_92-332865.pin
And this is the start of the contents of the first pin file:
SpecId Label ScanNr ExpMass CalcMass lnrSp deltLCn deltCn lnExpect Xcorr Sp IonFrac Mass PepLen Charge1 Charge2 Charge3 Charge4 Charge5 Charge6 enzN enzC enzInt lnNumSP dM absdM Peptide Proteins
/home/jannik/Masterthesis/data/Dataset_for_new_denovo_benchmark/PXD043200/WEC14392X002__S79_IGF_d1_92-332865_2_3_1 1 2 1336.735172 1335.726692 1.386294 0.000000 0.094556 4.801797 0.365910 0.905760 0.0500 1336.735172 11 0 0 1 0 0 0 1 1 2 8.697179 0.000755 0.000755 K.KTNLFKNVDEK.L sp|A8MVJ9|HPF1L_HUMAN
/home/jannik/Masterthesis/data/Dataset_for_new_denovo_benchmark/PXD043200/WEC14392X002__S79_IGF_d1_92-332865_7_3_1 1 7 904.574223 901.561799 0.000000 0.000000 0.007404 6.053122 0.157977 2.792109 0.0417 904.574223 7 0 0 1 0 0 0 1 1 2 7.623642 0.003341 0.003341 K.YHKVVKK.G sp|Q5TAP6|UT14C_HUMAN sp|Q9BVJ6|UT14A_HUMAN sp|Q9BVJ6-2|UT14A_HUMAN sp|Q9BVJ6-3|UT14A_HUMAN tr|X6RJY0|X6RJY0_HUMAN
/home/jannik/Masterthesis/data/Dataset_for_new_denovo_benchmark/PXD043200/WEC14392X002__S79_IGF_d1_92-332865_13_3_1 1 13 1009.650120 1007.647260 0.693147 0.000000 0.052369 6.906755 0.244918 2.399735 0.0312 1009.650120 9 0 0 1 0 0 0 1 1 2 6.152733 0.001988 0.001988 K.RRAAIPVPK.L sp|Q9NR23|GDF3_HUMAN
/home/jannik/Masterthesis/data/Dataset_for_new_denovo_benchmark/PXD043200/WEC14392X002__S79_IGF_d1_92-332865_21_3_1 1 21 1341.729374 1341.723338 1.386294 0.000000 0.003216 6.906755 0.241713 0.590729 0.0208 1341.729374 13 0 0 1 0 0 0 1 1 1 8.644002 0.000004 0.000004 R.DQGSGSRLGPIVR.R sp|Q9H8S5|CCNP_HUMAN tr|M0QZM5|M0QZM5_HUMAN sp|Q9H8S5-2|CCNP_HUMAN
...
I don't know whats wrong. Can someone help me?
Thanks for your time