ValueError: attempt to get argmin of an empty sequence

[mozammel47]

Dear Concern,

I am testing the pipeline with the microSplit data (SRR11940661) to implement to our sequence. However, running the split-seq I am facing an error. Could you please help me to solve the problem.

My command line:

split-seq all --fq1 /data/mhoque/03.transcriptomics/05.single_cell/SRR11940661_1.fastq.tar.gz \ --fq2 /data/mhoque/03.transcriptomics/05.single_cell/SRR11940661_2.fastq.tar.gz \ --output_dir /data/mhoque/03.transcriptomics/05.single_cell \ --chemistry v2 \ --genome_dir /data/mhoque/03.transcriptomics/05.single_cell/02.reference/Bacilus_subtilis/star_index \ --nthreads 4 \ --sample heatshock A1:B12 \ --sample control C1:D12 \ --splicing False

Prompt and error after running the command:

Namespace(bc_edit_dist='2', chemistry='v2', fasta=None, fq1='/data/mhoque/03.transcriptomics/05.single_cell/SRR11940661_1.fastq.tar.gz', fq2='/data/mhoque/03.transcriptomics/05.single_cell/SRR11940661_2.fastq.tar.gz', genes=None, genome=None, genomeSAindexNbases='14', genome_dir='/data/mhoque/03.transcriptomics/05.single_cell/02.reference/Bacilus_subtilis/star_index', mode='all', nthreads='4', output_dir='/data/mhoque/03.transcriptomics/05.single_cell', sample=[['heatshock', 'A1:B12'], ['control', 'C1:D12']], splicing='False', sublibraries=None, umi_threshold=0) all /data/mhoque/03.transcriptomics/05.single_cell/SRR11940661_1.fastq.tar.gz /data/mhoque/03.transcriptomics/05.single_cell/SRR11940661_2.fastq.tar.gz /data/mhoque/03.transcriptomics/05.single_cell v2 /data/mhoque/03.transcriptomics/05.single_cell/02.reference/Bacilus_subtilis/star_index None 2022-03-07 15:44:36.851051 Correcting barcodes... [10, 48, 78] 0 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000 1100000 1200000 1300000 1400000 1500000 1600000 1700000 1800000 1900000 Traceback (most recent call last): File "/data/mhoque/01.bio/05.soft/40.conda/miniconda/envs/python37/bin/split-seq", line 4, in import('pkg_resources').run_script('split-seq==0.0.1', 'split-seq') File "/data/mhoque/01.bio/05.soft/40.conda/miniconda/envs/python37/lib/python3.7/site-packages/pkg_resources/init.py", line 656, in run_script self.require(requires)[0].run_script(script_name, ns) File "/data/mhoque/01.bio/05.soft/40.conda/miniconda/envs/python37/lib/python3.7/site-packages/pkg_resources/init.py", line 1453, in run_script exec(code, namespace, namespace) File "/data/mhoque/01.bio/05.soft/40.conda/miniconda/envs/python37/lib/python3.7/site-packages/split_seq-0.0.1-py3.7.egg/EGG-INFO/scripts/split-seq", line 73, in tools.preprocess_fastq(args.fq1, args.fq2, args.output_dir, args.chemistry, args.bc_edit_dist) File "/data/mhoque/01.bio/05.soft/40.conda/miniconda/envs/python37/lib/python3.7/site-packages/split_seq-0.0.1-py3.7.egg/split_seq/tools.py", line 353, in preprocess_fastq counts,count_threshold = get_perfect_bc_counts(fastq2,n_reads=2000000,reads_in_cells_thresh=0.92) File "/data/mhoque/01.bio/05.soft/40.conda/miniconda/envs/python37/lib/python3.7/site-packages/split_seq-0.0.1-py3.7.egg/split_seq/tools.py", line 349, in get_perfect_bc_counts count_threshold = max(5, counts.iloc[abs(counts.cumsum()/counts.sum()-reads_in_cells_thresh).values.argmin()]) ValueError: attempt to get argmin of an empty sequence

Thanks Best regards Mozammel