Can't run example data - error "re-reun with the -g option for a genome file"

[natsampaio]

Hello,

I am trying to implement the FASTiCLIP package to analyse my data. However, I can't seem to get things to work with the example. There are a series of errors and the script aborts after around 15 min. I have set up an environment slightly differently from the instructions as follows:

$ conda create -n FASTiCLIP python=2
$ conda install matplotlib=1.5 pandas=0.18.1 samtools=0.1.18 bedtools=2.22.0 fastx_toolkit=0.0.14 matplotlib-venn=0.11.4 iclipro=0.1.1

Note: Bowtie2 ver 2.1.0 needs to be loaded via a module:
$ module load bowtie2/2.1.0

$ pip install git+https://github.com/ChangLab/FAST-iCLIP.git

$ export FASTICLIP_PATH=/t1-data/user/nsampaio/FASTiCLIP

Had to download the configure file to a new directory in my server space:
$ mkdir FASTiCLIP
$ cd FASTiCLIP
$ wget https://raw.githubusercontent.com/ChangLab/FAST-iCLIP/master/configure

Had to also manually download files in /bin, using wget as above, to new FASTiCLIP/bin directory

I ran command as follows (note, had to change from what is on the documentation because it doesn't match the example data now provided):

(FASTiCLIP) [nsampaio@klyn FASTiCLIP]$ fasticlip -i rawdata/A_Human_Test_R1.fastq rawdata/A_Human_Test_R2.fastq --GRCh38 -n MMhur -o results
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 625 sequences.
[samopen] SAM header is present: 625 sequences.
[samopen] no @sq lines in the header.
[sam_read1] missing header? Abort!
[samopen] no @sq lines in the header.
[sam_read1] missing header? Abort!
ERROR: Database file /t1-data/user/nsampaio/FASTiCLIP/docs/GRCh38/GRCh38_repeatMasker.bed contains chromosome chr1, but the query file does not.
Please re-reun with the -g option for a genome file.
See documentation for details.
ERROR: Database file /t1-data/user/nsampaio/FASTiCLIP/docs/GRCh38/GRCh38_repeatMasker.bed contains chromosome chr1, but the query file does not.
Please re-reun with the -g option for a genome file.
See documentation for details.
ERROR: Database file /t1-data/user/nsampaio/FASTiCLIP/docs/GRCh38/GRCh38_repeatMasker.bed contains chromosome chr1, but the query file does not.
Please re-reun with the -g option for a genome file.
See documentation for details.
ERROR: Database file /t1-data/user/nsampaio/FASTiCLIP/docs/GRCh38/GRCh38_repeatMasker.bed contains chromosome chr1, but the query file does not.
Please re-reun with the -g option for a genome file.
See documentation for details.
Error: Unable to open file /t1-data/user/nsampaio/FASTiCLIP/docs/GRCh38/snoRNA_coordinates_15exp.bed. Exiting.
Error: Unable to open file /t1-data/user/nsampaio/FASTiCLIP/docs/GRCh38/snoRNA_coordinates_15exp.bed. Exiting.
ERROR: Database file /t1-data/user/nsampaio/FASTiCLIP/docs/GRCh38/miR_sort_clean.bed contains chromosome chr1, but the query file does not.
Please re-reun with the -g option for a genome file.
See documentation for details.
ERROR: Database file /t1-data/user/nsampaio/FASTiCLIP/docs/GRCh38/genes_BED6.bed contains chromosome chr1, but the query file does not.
Please re-reun with the -g option for a genome file.
See documentation for details.
needLargeMem: trying to allocate 0 bytes (limit: 17179869184)
needLargeMem: trying to allocate 0 bytes (limit: 17179869184)
needLargeMem: trying to allocate 0 bytes (limit: 17179869184)
Traceback (most recent call last):
File "/t1-data/user/nsampaio/py36-v1/conda-install/envs/FASTiCLIP/bin/fasticlip", line 11, in
load_entry_point('fasticlip==0.9.3', 'console_scripts', 'fasticlip')()
File "/t1-data/user/nsampaio/py36-v1/conda-install/envs/FASTiCLIP/lib/python2.7/site-packages/fasticlip/fasticlip.py", line 331, in main
geneCounts_pc = get_gene_counts(proteinCodingReads_centered)
File "/t1-data/user/nsampaio/py36-v1/conda-install/envs/FASTiCLIP/lib/python2.7/site-packages/fasticlip/helper.py", line 570, in get_gene_counts
bf=pd.DataFrame(pd.read_table(bedFile,header=None))
File "/t1-data/user/nsampaio/py36-v1/conda-install/envs/FASTiCLIP/lib/python2.7/site-packages/pandas/io/parsers.py", line 562, in parser_f
return _read(filepath_or_buffer, kwds)
File "/t1-data/user/nsampaio/py36-v1/conda-install/envs/FASTiCLIP/lib/python2.7/site-packages/pandas/io/parsers.py", line 315, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/t1-data/user/nsampaio/py36-v1/conda-install/envs/FASTiCLIP/lib/python2.7/site-packages/pandas/io/parsers.py", line 645, in init
self._make_engine(self.engine)
File "/t1-data/user/nsampaio/py36-v1/conda-install/envs/FASTiCLIP/lib/python2.7/site-packages/pandas/io/parsers.py", line 799, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/t1-data/user/nsampaio/py36-v1/conda-install/envs/FASTiCLIP/lib/python2.7/site-packages/pandas/io/parsers.py", line 1213, in init
self._reader = _parser.TextReader(src, **kwds)
File "pandas/parser.pyx", line 523, in pandas.parser.TextReader.cinit (pandas/parser.c:5214)
pandas.io.common.EmptyDataError: No columns to parse from file

[izarvillasante]

I am having the same issue