The --technology flag does not seem to be working correctly

[davidmarcus]

--technology does not seem to be a recognized argument.

Easily reproducible using the packaged example:

(ena_env) ubuntu@ip-172-31-33-107:~/example$ ../splash --technology base --bin_path .. input.txt
usage: splash [-h] [--outname_prefix OUTNAME_PREFIX] [--anchor_len ANCHOR_LEN] [--gap_len GAP_LEN] [--target_len TARGET_LEN] [--anchor_list ANCHOR_LIST]
              [--pvals_correction_col_name PVALS_CORRECTION_COL_NAME] [--without_compactors] [--compactors_config COMPACTORS_CONFIG] [--poly_ACGT_len POLY_ACGT_LEN] [--artifacts ARTIFACTS]
              [--dont_filter_illumina_adapters] [--anchor_unique_targets_threshold ANCHOR_UNIQUE_TARGETS_THRESHOLD] [--anchor_count_threshold ANCHOR_COUNT_THRESHOLD]
              [--anchor_samples_threshold ANCHOR_SAMPLES_THRESHOLD] [--anchor_sample_counts_threshold ANCHOR_SAMPLE_COUNTS_THRESHOLD] [--n_most_freq_targets_for_stats N_MOST_FREQ_TARGETS_FOR_STATS]
              [--fdr_threshold FDR_THRESHOLD] [--min_hamming_threshold MIN_HAMMING_THRESHOLD] [--keep_top_n_target_entropy KEEP_TOP_N_TARGET_ENTROPY] [--dump_Cjs]
              [--max_pval_opt_for_Cjs MAX_PVAL_OPT_FOR_CJS] [--n_most_freq_targets N_MOST_FREQ_TARGETS] [--with_effect_size_cts] [--with_pval_asymp_opt] [--without_seqence_entropy]
              [--sample_name_to_id SAMPLE_NAME_TO_ID] [--dump_sample_anchor_target_count_txt] [--dump_sample_anchor_target_count_binary] [--supervised_test_samplesheet SUPERVISED_TEST_SAMPLESHEET]
              [--supervised_test_anchor_sample_fraction_cutoff SUPERVISED_TEST_ANCHOR_SAMPLE_FRACTION_CUTOFF] [--supervised_test_num_anchors SUPERVISED_TEST_NUM_ANCHORS] [--opt_num_inits OPT_NUM_INITS]
              [--opt_num_iters OPT_NUM_ITERS] [--num_rand_cf NUM_RAND_CF] [--num_splits NUM_SPLITS] [--opt_train_fraction OPT_TRAIN_FRACTION] [--without_alt_max] [--bin_path BIN_PATH]
              [--tmp_dir TMP_DIR] [--n_threads_stage_1 N_THREADS_STAGE_1] [--n_threads_stage_1_internal N_THREADS_STAGE_1_INTERNAL] [--n_threads_stage_1_internal_boost N_THREADS_STAGE_1_INTERNAL_BOOST]
              [--n_threads_stage_2 N_THREADS_STAGE_2] [--n_bins N_BINS] [--kmc_use_RAM_only_mode] [--kmc_max_mem_GB KMC_MAX_MEM_GB] [--dont_clean_up] [--logs_dir LOGS_DIR]
              input_file
splash: error: unrecognized arguments: --technology input.txt

[marekkokot]

Hi, thanks!
Could you let me know if you are sure you are using the newest version?
I have just tried the newest release, and it seems to work.

wget https://github.com/refresh-bio/SPLASH/releases/download/v2.11.6/splash-2.11.6.linux.x64.tar.gz
tar -xvf splash-2.11.6.linux.x64.tar.gz
cd example
./download.py
../splash --technology base --bin_path .. input.txt

Output:

Welcome to SPLASH
Version:  2.11.6
Current time: 2025-02-21 08:56:35
----------------  Configuration  ---------------
input_file: input.txt
outname_prefix: result
anchor_len: 31
gap_len: 0
target_len: 31
anchor_list: 
pvals_correction_col_name: pval_opt
technology: base
without_compactors: False
compactors_config: 
lookup_table_config: 
poly_ACGT_len: 8
artifacts: 
dont_filter_illumina_adapters: False
anchor_unique_targets_threshold: 1
anchor_count_threshold: 50
anchor_samples_threshold: 1
anchor_sample_counts_threshold: 5
n_most_freq_targets_for_stats: 0
n_most_freq_targets_for_dump: 0
fdr_threshold: 0.05
min_hamming_threshold: 0
keep_top_n_target_entropy: 10000
keep_top_n_effect_size_bin: 20000
keep_significant_anchors_satc: False
keep_top_target_entropy_anchors_satc: False
keep_top_effect_size_bin_anchors_satc: False
dump_Cjs: False
max_pval_opt_for_Cjs: 0.1
n_most_freq_targets: 10
with_effect_size_cts: False
with_pval_asymp_opt: False
without_seqence_entropy: False
sample_name_to_id: sample_name_to_id.mapping.txt
dump_sample_anchor_target_count_txt: False
dump_sample_anchor_target_count_binary: False
satc_merge_dump_format: splash
supervised_test_samplesheet: 
supervised_test_anchor_sample_fraction_cutoff: 0.4
supervised_test_num_anchors: 20000
opt_num_inits: 10
opt_num_iters: 50
num_rand_cf: 50
num_splits: 1
opt_train_fraction: 0.25
without_alt_max: False
without_sample_spectral_sum: False
compute_also_old_base_pvals: False
Cjs_samplesheet: 
bin_path: ..
tmp_dir: 
n_threads_stage_1: 0
n_threads_stage_1_internal: 0
n_threads_stage_1_internal_boost: 1
n_threads_stage_2: 0
n_bins: 128
kmc_use_RAM_only_mode: False
kmc_max_mem_GB: 12
dont_clean_up: False
logs_dir: logs
cbc_len: 16
umi_len: 12
soft_cbc_umi_len_limit: 0
cbc_filtering_thr: 0
cell_type_samplesheet: 
export_cbc_logs: False
predefined_cbc: 
export_filtered_input: False
allow_strange_cbc_umi_reads: False
postprocessing_item: []
exclude_postprocessing_item: None
REMOVE_INPUT: False
------------------------------------------------
n_threads_stage_1 auto adjusted to 4
n_threads_stage_1_internal auto adjusted to 16
n_threads_stage_2 auto adjusted to 64
Starting stage 1
Current time: 2025-02-21 08:56:35
Stage 1 done
Starting stage 2
Current time: 2025-02-21 08:56:39
Stage 2 done
Starting stage 3
Current time: 2025-02-21 08:56:40
Stage 3 done
Start top target entropy select
Current time: 2025-02-21 08:56:41
Top target entropy select done
Start top effect_size_bin select
Current time: 2025-02-21 08:56:41
Effect size bin select done
Starting compactors
Current time: 2025-02-21 08:56:41
compactors done
SPLASH finished!
Current time: 2025-02-21 08:56:48

BTW. usually you don't need to specify --bin_path