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Error: Cannot open file result_satc/bin-1.satc to get file size #14

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abora101 opened this issue Jan 10, 2024 · 0 comments
Open

Error: Cannot open file result_satc/bin-1.satc to get file size #14

abora101 opened this issue Jan 10, 2024 · 0 comments

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@abora101
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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.

Do you know what the issue is?

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