issue with PAScall

[lakewoo]

Hi,

I ran into an issue when running PAScall with the test dataset PBMC3K. The DeepPASS.predict step throw an error list below. I got the outputs as PBMC3k.*.peaks.annotated.bed with just few lines, and then the program stopped.

Thank you for your help in advance!

##############

Here is the log file from "PBMC3K.exonic.peaks.DeepPASS.predict.log":

2022-10-19 13:04:06.688118: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2699950000 Hz
2022-10-19 13:04:06.693677: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55fd635f5ef0 executing computations on platform Host. Devices:
2022-10-19 13:04:06.693779: I tensorflow/compiler/xla/service/service.cc:175] StreamExecutor device (0): Host, Default Version
2022-10-19 13:04:06.718258: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/lib:/usr/local/lib:/usr/local/gmp/5.1.1/lib64:/gpfs/tools/gsl/lib:/gpfs/tools/icu58/lib/:/gpfs/tools/anaconda/lib:/gpfs/tools/gsl/lib:/gpfs/tools/libiconv-1.15/lib
2022-10-19 13:04:06.718430: E tensorflow/stream_executor/cuda/cuda_driver.cc:318] failed call to cuInit: UNKNOWN ERROR (303)
2022-10-19 13:04:06.718510: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (amber): /proc/driver/nvidia/version does not exist

********************** Start Data Processing **************************
Traceback (most recent call last):
File "/home/jt/gpfs_analyses/Hao/SCAPTURE/DeepPASS/Predict.py", line 69, in
dataset_pre = pd.read_csv(pre_f,sep='\t',index_col = False,header = None)
File "/gpfs/tools/anaconda/envs/SCAPTURE_env/lib/python3.7/site-packages/pandas/io/parsers.py", line 676, in parser_f
return _read(filepath_or_buffer, kwds)
File "/gpfs/tools/anaconda/envs/SCAPTURE_env/lib/python3.7/site-packages/pandas/io/parsers.py", line 448, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/gpfs/tools/anaconda/envs/SCAPTURE_env/lib/python3.7/site-packages/pandas/io/parsers.py", line 880, in init
self._make_engine(self.engine)
File "/gpfs/tools/anaconda/envs/SCAPTURE_env/lib/python3.7/site-packages/pandas/io/parsers.py", line 1114, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/gpfs/tools/anaconda/envs/SCAPTURE_env/lib/python3.7/site-packages/pandas/io/parsers.py", line 1891, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 532, in pandas._libs.parsers.TextReader.cinit
pandas.errors.EmptyDataError: No columns to parse from file

And Here is the log file from PBMC3k.PAScall.log:
scapture path: /home/SCAPTURE/
DeepPASS model file dir: /home/SCAPTURE//DeepPASS/
scapture module: PAScall
Output prefix: PBMC3k
prefix of annotation files from annotation module: ../annotation/SCAPTURE_annotation
BAM file: ./PBMC3k.test.bam
Fragment length: 98
GENOME file: ../annotation/GRCh38.p13.genome.fa
Peak width: 400
OverlapRatio: 0.5
threads: 16
poly(a) database file: ../SupTab_KnownPASs_fourDBs.txt
scapture PAScall: create command line. Wed Oct 19 18:14:26 PDT 2022
scapture PAScall: create command line done. Wed Oct 19 18:14:35 PDT 2022
scapture PAScall: peak calling. Wed Oct 19 18:14:35 PDT 2022
scapture PAScall: peak calling done. Wed Oct 19 18:17:07 PDT 2022
scapture PAScall: peak annotating. Wed Oct 19 18:17:07 PDT 2022
scapture PAScall: peak annotating done. Wed Oct 19 18:17:13 PDT 2022
scapture PAScall: PAS evaluating. Wed Oct 19 18:17:13 PDT 2022

Tool: bedtools getfasta (aka fastaFromBed)
Version: v2.25.0
Summary: Extract DNA sequences into a fasta file based on feature coordinates.

Usage: bedtools getfasta [OPTIONS] -fi -bed <bed/gff/vcf> -fo

Options:
-fi Input FASTA file
-bed BED/GFF/VCF file of ranges to extract from -fi
-fo Output file (can be FASTA or TAB-delimited)
-name Use the name field for the FASTA header
-split given BED12 fmt., extract and concatenate the sequencesfrom the BED "blocks" (e.g., exons)
-tab Write output in TAB delimited format.
- Default is FASTA format.

-s	Force strandedness. If the feature occupies the antisense,
	strand, the sequence will be reverse complemented.
	- By default, strand information is ignored.

-fullHeader	Use full fasta header.
	- By default, only the word before the first space or tab is used.

cat: PBMC3k.exonic.peaks.DeepPASS.predictout/Predict_Result.txt: No such file or directory
.....
cat: PBMC3k.intronic.peaks.DeepPASS.predictout/Predict_Result.txt: No such file or directory
...
cat: PBMC3k.3primeExtended.peaks.DeepPASS.predictout/Predict_Result.txt: No such file or directory
***** ERROR: too many digits/characters for integer conversion in string . Exiting...
scapture PAScall: output files -- PBMC3k.exonic.peaks.evaluated.bed PBMC3k.intronic.peaks.evaluated.bed PBMC3k.3primeExtended.peaks.evaluated.bed
scapture PAScall: PAS evaluating done. Wed Oct 19 18:18:26 PDT 2022

[liguowei-CAS]

Plz try the command below in your environment to check bedtools :

bedtools getfasta -fi /Your_Path_To/genome.fa -bed PBMC3k.exonic.peaks.annotated.bed -s -split -name > PBMC3k.exonic.peaks.annotated.fa
We recommend bedtools 2.26.0 for SCAPTURE:
conda install -c biobuilds bedtools
If I can be of assistance, please do not hesitate to contact me.