vetmohit89
commented
6 months ago Have you tested the pipeline with test dataset? I have provided MALAT1 RNA treated with PUS7 enzyme fastq files and MALAT1 sequence.
Try running NanoPsiPy_estimation with this dataset first.
Thank you Mohit
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From: Elton Vasconcelos @.> Sent: Wednesday, May 8, 2024 9:06:15 AM To: vetmohit89/NanoPsiPy @.> Cc: Subscribed @.***> Subject: [vetmohit89/NanoPsiPy] no alignment generated (Issue #3)
Hello,
Thanks for the tool! I'm encountering a problem on the NanoPsiPy_estimation step. It seems that the alignment outputs are not generated, as the "alignment" folder contains only an empty features.csv file, and no "plus_strand" nor "minus_strand" subfolders.
$ NanoPsiPy_estimation -i ../rawData/pus1ko/pus1ko-r1/20240228_1330_MC-116134_FAY49401_30e62174/fastq_pass/ -r ../../refGenome/GQ994935.fasta -o pus1ko_estimation.tsv -s treatment
[M::mm_idx_gen::0.0161.16] collected minimizers [M::mm_idx_gen::0.0261.82] sorted minimizers [M::main::0.0271.79] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.0291.73] mid_occ = 26 [M::mm_idx_stat] kmer size: 14; skip: 5; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.031*1.68] distinct minimizers: 45492 (99.22% are singletons); average occurrences: 1.027; average spacing: 2.957; total leng th: 138146 [M::main] Version: 2.18-r1015 [M::main] CMD: minimap2 -ax splice -uf -k14 --secondary=no/../../refGenome/GQ994935 .psu/nanoPsiPy-run/temp/all_pass_fastq.fastq [M::main] Real time: 0.038 sec; CPU: 0.057 sec; Peak RSS: 0.008 GB
Traceback (most recent call last): File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/nanoPsiPy/bin/NanoPsiPy_estimation", line 48, in ex_fe() File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/nanoPsiPy/lib/python3.11/site-packages/NanoPsiPy/Pseudo_U_estimation.pyhttps://urldefense.com/v3/__http://Pseudo_U_estimation.py__;!!NoSwA-eRAg!BDNGY-FpuwBvxHECYeE6a6Vx8_1wv20UbzemqEjbLgNEHhhjdPboX1yUUAqFcbYtU-Y3tMPh2K_WOK0Ky0t7wu4N$", line 105, in ex_fe with open(plus_file, "r") as input_file: ^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: '.psu/nanoPsiPy-run/alignment/plus_strand/collect_pile_no_intron.txt'
Any light to shed? Thanks
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eltonjrv
Hello,
Thanks for the tool! I'm encountering a problem on the NanoPsiPy_estimation step. It seems that the alignment outputs are not generated, as the "alignment" folder contains only an empty features.csv file, and no "plus_strand" nor "minus_strand" subfolders.
$ NanoPsiPy_estimation -i ../rawData/pus1ko/pus1ko-r1/20240228_1330_MC-116134_FAY49401_30e62174/fastq_pass/ -r ../../refGenome/GQ994935.fasta -o pus1ko_estimation.tsv -s treatment
[M::mm_idx_gen::0.0161.16] collected minimizers [M::mm_idx_gen::0.0261.82] sorted minimizers [M::main::0.0271.79] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.0291.73] mid_occ = 26 [M::mm_idx_stat] kmer size: 14; skip: 5; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.031*1.68] distinct minimizers: 45492 (99.22% are singletons); average occurrences: 1.027; average spacing: 2.957; total leng th: 138146 [M::main] Version: 2.18-r1015 [M::main] CMD: minimap2 -ax splice -uf -k14 --secondary=no/../../refGenome/GQ994935 .psu/nanoPsiPy-run/temp/all_pass_fastq.fastq [M::main] Real time: 0.038 sec; CPU: 0.057 sec; Peak RSS: 0.008 GB
Traceback (most recent call last): File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/nanoPsiPy/bin/NanoPsiPy_estimation", line 48, in
ex_fe()
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/nanoPsiPy/lib/python3.11/site-packages/NanoPsiPy/Pseudo_U_estimation.py", line 105, in ex_fe
with open(plus_file, "r") as input_file:
^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '.psu/nanoPsiPy-run/alignment/plus_strand/collect_pile_no_intron.txt'
Any light to shed? Thanks