We get an error when trying to load a table that's too wide for MySQL (InnoDB storage engine) ERROR 1117 (HY000) at line 26: Too many columns We are aware that this wide a table was a bad idea (http://dba.stackexchange.com/questions/3972/too-many-columns-in-mysql) but need to get this to work because of legacy data.
# Dummy example
wget https://gist.githubusercontent.com/shntnu/2063640233023746222ce83bdb954e12/raw/33574c30f0638f7ac8dfca3e6ad8abbb83c4003e/wide_table.sql
mysql -u root --execute="create database wide_test;"
mysql -u root wide_test < wide_table.sql
#> ERROR 1117 (HY000) at line 1: Too many columns
# Real example
echo "http://pubs.broadinstitute.org/bray_natprot_2016/suppl/online/seedseq_data/seedseq_per_cells.sql.gz
http://pubs.broadinstitute.org/bray_natprot_2016/suppl/online/seedseq_data/seedseq_per_cytoplasm.sql.gz
http://pubs.broadinstitute.org/bray_natprot_2016/suppl/online/seedseq_data/seedseq_per_nuclei.sql.gz
http://pubs.broadinstitute.org/bray_natprot_2016/suppl/online/seedseq_data/seedseq_per_image.sql.gz
https://github.com/carpenterlab/2016_bray_natprot/raw/master/supplementary_files/seedseq_per_object.sql.gz" > files.txt
wget -i files.txt
cat files.txt | sed 's/\(.*\)\(seedseq.*\)/\2/g'|xargs -I % echo gunzip %
#mysql Ver 14.14 Distrib 5.5.54, for debian-linux-gnu (x86_64) using readline 6.3
mysql -u root --execute="create database natprot;"
mysql -u root natprot < seedseq_per_image.sql
mysql -u root natprot < seedseq_per_nuclei.sql
mysql -u root natprot < seedseq_per_cells.sql
mysql -u root natprot < seedseq_per_cytoplasm.sql
# this fails ERROR 1117 (HY000) at line 26: Too many columns
mysql -u root natprot < seedseq_per_object.sql