ERROR:lib.tools:1, in line 2. Skipping line... ERROR:lib.tools:49151, in line 49152. Skipping line...

[Bio-info-ai]

Hi,

I am using SUPPA to analyse DAS in rice.

My gtf file was generated from ESPRESSO:

ESPRESSO version: 1.4.0, source code commit: unknown

Chr07 annotated_isoform transcript 3258629 3261815 . + . transcript_id "AGIS_Os07g005390.mRNA1"; gene_id "AGIS_Os07g0053>
Chr07 annotated_isoform exon 3258629 3258826 . + . transcript_id "AGIS_Os07g005390.mRNA1"; gene_id "AGIS_Os07g005390"; exo>
Chr07 annotated_isoform exon 3258952 3259053 . + . transcript_id "AGIS_Os07g005390.mRNA1"; gene_id "AGIS_Os07g005390"; exo>
Chr07 annotated_isoform exon 3261019 3261176 . + . transcript_id "AGIS_Os07g005390.mRNA1"; gene_id "AGIS_Os07g005390"; exo>
Chr07 annotated_isoform exon 3261319 3261815 . + . transcript_id "AGIS_Os07g005390.mRNA1"; gene_id "AGIS_Os07g005390"; exo>
...
Chr07 novel_isoform transcript 2018957 2024237 . + . transcript_id "ESPRESSO:Chr07:285:783"; gene_id "AGIS_Os07g003450";
Chr07 novel_isoform exon 2018957 2019052 . + . transcript_id "ESPRESSO:Chr07:285:783"; gene_id "AGIS_Os07g003450"; exon_number>
Chr07 novel_isoform exon 2019208 2019312 . + . transcript_id "ESPRESSO:Chr07:285:783"; gene_id "AGIS_Os07g003450"; exon_number>
Chr07 novel_isoform exon 2019998 2020059 . + . transcript_id "ESPRESSO:Chr07:285:783"; gene_id "AGIS_Os07g003450"; exon_number>
Chr07 novel_isoform exon 2020141 2020224 . + . transcript_id "ESPRESSO:Chr07:285:783"; gene_id "AGIS_Os07g003450"; exon_number>
Chr07 novel_isoform exon 2020311 2020526 . + . transcript_id "ESPRESSO:Chr07:285:783"; gene_id "AGIS_Os07g003450"; exon_number>
Chr07 novel_isoform exon 2021995 2022223 . + . transcript_id "ESPRESSO:Chr07:285:783"; gene_id "AGIS_Os07g003450"; exon_number>
Chr07 novel_isoform exon 2022943 2023170 . + . transcript_id "ESPRESSO:Chr07:285:783"; gene_id "AGIS_Os07g003450"; exon_number>
Chr07 novel_isoform exon 2023333 2023634 . + . transcript_id "ESPRESSO:Chr07:285:783"; gene_id "AGIS_Os07g003450"; exon_number>
Chr07 novel_isoform exon 2023750 2024237 . + . transcript_id "ESPRESSO:Chr07:285:783"; gene_id "AGIS_Os07g003450"; exon_number>

My XXX_iso_tpm.txt file look like this:

Sy1_RD15_20DAF_1_quant Sy1_RD15_20DAF_2_quant Sy1_RD15_20DAF_3_quant Sy2_RD15_20DAF_1_quant Sy2_RD15_20DAF_2_quant Sy2_RD15_20DAF_3_quant
AGIS_Os07g000020.mRNA1 5.247624 7.114523 7.309581 23.678155 19.538376 20.639924
AGIS_Os07g000030.mRNA1 3.413129 3.015613 2.981317 10.347559 10.669533 11.116893
AGIS_Os07g000060.mRNA1 0.940469 0.669432 1.494167 4.210912 2.712298 2.917053
AGIS_Os07g000060.mRNA2 0.135438 0.118135 0.14009 0.13705 0.344516 0
ESPRESSO:Chr07:285:701 0.456516 0.217173 0.220987 0.363377 0.778716 0
AGIS_Os07g000060.mRNA3 1.52254 2.021065 1.874106 7.830967 7.375092 9.832155
AGIS_Os07g000070.mRNA1 0.024991 0.063043 0.124003 0.128176 0 0.131997
AGIS_Os07g000090.mRNA1 0.026463 0.021891 0.084936 0.099728 0 0.104516
AGIS_Os07g000090.mRNA2 0 0 0 0 0 0
ESPRESSO:Chr07:285:925 0 0 0 0 0.25583 0
AGIS_Os07g000100.mRNA1 0.042203 0 0 0 0.068915 0
AGIS_Os07g000100.mRNA2 0.232741 0.196573 0.385143 0.87086 0.981609 1.127819
ESPRESSO:Chr07:285:555 0 0 0 0 0 0
ESPRESSO:Chr07:285:388 0.883809 0.440658 0.17614 0.260479 0.506969 0.741765
ESPRESSO:Chr07:285:387 0 0.936567 1.084685 5.110703 4.079722 3.859722
AGIS_Os07g000120.mRNA1 1.242568 1.920928 1.677653 4.276167 3.599262 4.656542
ESPRESSO:Chr07:285:556 0.481966 0.436255 0.479257 0.991119 1.999671 0.248109

I ran into this ERROR when I calculate PSI:

INFO:lib.tools:File XXX_iso_tpm.txt opened in reading mode.
INFO:psiCalculator:Buffering transcript expression levels.
ERROR:lib.tools:1, in line 2. Skipping line...
ERROR:lib.tools:2, in line 3. Skipping line...
ERROR:lib.tools:3, in line 4. Skipping line...
ERROR:lib.tools:4, in line 5. Skipping line...
ERROR:lib.tools:5, in line 6. Skipping line...
ERROR:lib.tools:6, in line 7. Skipping line...
ERROR:lib.tools:7, in line 8. Skipping line...
ERROR:lib.tools:8, in line 9. Skipping line...
ERROR:lib.tools:9, in line 10. Skipping line...
ERROR:lib.tools:10, in line 11. Skipping line...
ERROR:lib.tools:11, in line 12. Skipping line...
ERROR:lib.tools:12, in line 13. Skipping line...
ERROR:lib.tools:13, in line 14. Skipping line...
ERROR:lib.tools:14, in line 15. Skipping line...
...
ERROR:lib.tools:49144, in line 49145. Skipping line...
ERROR:lib.tools:49145, in line 49146. Skipping line...
ERROR:lib.tools:49146, in line 49147. Skipping line...
ERROR:lib.tools:49147, in line 49148. Skipping line...
ERROR:lib.tools:49148, in line 49149. Skipping line...
ERROR:lib.tools:49149, in line 49150. Skipping line...
ERROR:lib.tools:49150, in line 49151. Skipping line...
ERROR:lib.tools:49151, in line 49152. Skipping line...
INFO:lib.tools:File XXX_iso_tpm.txt closed.
ERROR:psiCalculator:No expression values have been buffered.
ERROR:psiCalculator:Unknown error: 1

Thank you for your help!

[leipzig]

what does XXX_iso_tpm.txt look like?