issue with chrom sizes

[mistrm82]

Hi,

I am trying to run this script and am successful to the point of "Generating spike normalized bedgraphs". At this point it doesn't seem to like my chrom_sizes file and it would be great if you can clarify the input here. I am using GRCh37 and so I gave a tab-delimited text based file where column 1 is the chromosome, column 2 is the size. I tried with and without a header. I also changed the name of the file (because it seems it adds the suffix ".chromInfo". Below is the code I used and the error I get. Any help would be very much appreciated.

Thank you!
Meeta

# Run the script 
 python -c 'import py_sam_2_spikenormbg; py_sam_2_spikenormbg.spikenormbg(folder="/n/data1/cores/bcbio/PIs/eric_greer/greer_rnaseq_cutnrun_analysis_of_microprotein_hbc04238/cutnrun/heinikoff/test_run", spike_suffix="yeast", input_type ="bam", chrom_sizes="/n/data1/cores/bcbio/PIs/eric_greer/greer_rnaseq_cutnrun_analysis_of_microprotein_hbc04238/cutnrun/heinikoff/GRCh37")'

Generating spike normalized bedgraphs from all the bed files

spike counts:
[32.0]
b"ERROR 1064 (42000) at line 1: You have an error in your SQL syntax; check the manual that corresponds to your MariaDB server version for the right syntax to use near '/n/data1/cores/bcbio/PIs/eric_greer/greer_rnaseq_cutnrun_analysis_of_micropro...' at line 1\n"
Commands were:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom, size from /n/data1/cores/bcbio/PIs/eric_greer/greer_rnaseq_cutnrun_analysis_of_microprotein_hbc04238/cutnrun/heinikoff/GRCh37.chromInfo"

[mistrm82]

I am providing a file, so it shouldn't be accessing the sql server, I am just not sure how to edit the command so it recognizes that I am giving a file as input