Hello, I am running splash2 with the following command: splash --n_bins 4 --kmc_use_RAM_only_mode --supervised_test_samplesheet /work/09657/abora32/ls6/supervised_test_with_cutadapted_data/supervised_samplesheet.txt /work/09657/abora32/ls6/supervised_test_with_cutadapted_data/cutadapted_input_data.txt
The unsupervised test runs correctly, but the supervised test returns an error. This is the error:
input : result_satc/bin-1.satc
output : ./supervised_test_supervised_metadata/satcOut-1.tsv
anchor_list : ./supervised_test_supervised_metadata/selected_anchors_GLMnet.txt
sample_names :
n_bins : 0
separately : false
format : satc
Error: cannot open file result_satc/bin-1.satc to get file size
input : result_satc/bin0.satc
output : ./supervised_test_supervised_metadata/satcOut0.tsv
anchor_list : ./supervised_test_supervised_metadata/selected_anchors_GLMnet.txt
sample_names :
n_bins : 0
separately : false
format : satc
Error: cannot open file result_satc/bin0.satc to get file size
input : result_satc/bin1.satc
output : ./supervised_test_supervised_metadata/satcOut1.tsv
anchor_list : ./supervised_test_supervised_metadata/selected_anchors_GLMnet.txt
sample_names :
n_bins : 0
separately : false
format : satc
Error: cannot open file result_satc/bin1.satc to get file size
input : result_satc/bin2.satc
output : ./supervised_test_supervised_metadata/satcOut2.tsv
anchor_list : ./supervised_test_supervised_metadata/selected_anchors_GLMnet.txt
sample_names :
n_bins : 0
separately : false
format : satc
Error: cannot open file result_satc/bin2.satc to get file size
input : result_satc/bin3.satc
output : ./supervised_test_supervised_metadata/satcOut3.tsv
anchor_list : ./supervised_test_supervised_metadata/selected_anchors_GLMnet.txt
sample_names :
n_bins : 0
separately : false
format : satc
Error: cannot open file result_satc/bin3.satc to get file size
Error in fread(paste(directory, "/", run_name, "_supervised_metadata/", :
File './supervised_test_supervised_metadata/NA' does not exist or is non-readable. getwd()=='/work/09657/abora32/ls6/spv_3'
Calls: rbind -> rbind -> lapply -> fread
Execution halted
Command exited with non-zero status 1
I have tried multiple --n_bins sizes and with/without the --kmc_use_RAM_only_mode flag. Unlike some similar problems which have been posted, my system is currently on a very high ulimit -n (about 2^20) and has high memory.
Hello, I am running splash2 with the following command: splash --n_bins 4 --kmc_use_RAM_only_mode --supervised_test_samplesheet /work/09657/abora32/ls6/supervised_test_with_cutadapted_data/supervised_samplesheet.txt /work/09657/abora32/ls6/supervised_test_with_cutadapted_data/cutadapted_input_data.txt
The unsupervised test runs correctly, but the supervised test returns an error. This is the error:
I have tried multiple --n_bins sizes and with/without the --kmc_use_RAM_only_mode flag. Unlike some similar problems which have been posted, my system is currently on a very high ulimit -n (about 2^20) and has high memory.
Do you know what the issue is?