Hello,
thank you for providing this excellent tool, but I encountered some unexpected errors while running it. My Nextflow pipeline only executed the first six steps, then skipped the remaining steps and stopped without showing any errors. Do you have any idea what might be causing this issue?
Below is my output.
executor > local (81)
[2f/41f167] ann…mon_transcriptome_indexing | 1 of 1 ✔
[89/08bd79] ann…illumina_single_cell_E3-2) | 2 of 2 ✔
[7b/c81ad2] ann…mina_single_cell_E3-2.sf]) | 1 of 1 ✔
[35/e4a853] ann…g (chr1, merge_quants.txt) | 25 of 25 ✔
[d6/dc0b47] rea…illumina_single_cell_E3-2) | 2 of 2 ✔
[95/ffd322] rea…na_single_cell_E3-2, chr1) | 50 of 50 ✔
[- ] rea…cessing:bedfile_conversion -
[- ] rea…eads_mapping_and_filtering -
[- ] reads_processing:ip_splitting -
[- ] reads_processing:ip_filtering -
[- ] iso…n:probability_distribution -
[- ] iso…ion:fragment_probabilities -
[- ] iso…tification:cells_splitting -
[- ] iso…uantification:em_algorithm -
[- ] iso…antification:cells_merging -
[- ] iso…ntification:dge_generation -
[- ] apa…differential_isoform_usage -
[- ] apa…n:generation_filtered_bams -
Completed at: 24-Apr-2026 12:13:33
Duration : 2h 55m 41s
CPU hours : 13.0
Succeeded : 81
Below is my input.
nextflow run -resume SCALPEL/main.nf
--sequencing chromium
--samplesheet /scratch/fengzhanmiao/benchmark/scKenver/SCALPEL_need/samplesheet.csv
--transcriptome /scratch/fengzhanmiao/benchmark/scKenver/gencode.v49.transcripts.fa.gz
--gtf /scratch/fengzhanmiao/benchmark/scKenver/gencode.v49.annotation.gtf.gz
--barcodes /scratch/fengzhanmiao/benchmark/scKenver/SCALPEL_need/whitelist_barcodes.csv
--ipdb /scratch/fengzhanmiao/benchmark/scKenver/refdata-gex-GRCh38-2020-A.polyA.track
--cpus 32
--outputDir 1_SCALPEl_output
Below is the content of my samples.tsv file.
0_clean_illumina_single_cell_E3-2,/scratch/fengzhanmiao/benchmark/scKenver/0_data-clean/illumina-clean/illumina_single_cell_E3-2_S6_R1_001.fastq.gz,/scratch/fengzhanmiao/benchmark/scKenver/0_data-clean/illumina-clean/illumina_single_cell_E3-2_S6_R2_001.fastq.gz,/scratch/fengzhanmiao/benchmark/scKenver/0_clean_illumina_single_cell_E3-2
0_clean_illumina_single_cell_E3-3,/scratch/fengzhanmiao/benchmark/scKenver/0_data-clean/illumina-clean/illumina_single_cell_E3-3_S10_R1_001.fastq.gz,/scratch/fengzhanmiao/benchmark/scKenver/0_data-clean/illumina-clean/illumina_single_cell_E3-3_S10_R2_001.fastq.gz,/scratch/fengzhanmiao/benchmark/scKenver/0_clean_illumina_single_cell_E3-3
Below is the content of my barcodes.tsv file.
0_clean_illumina_single_cell_E3-2,/scratch/fengzhanmiao/benchmark/scKenver/3M-february-2018.txt
0_clean_illumina_single_cell_E3-3,/scratch/fengzhanmiao/benchmark/scKenver/3M-february-2018.txt
I would be very grateful if you could take some time to help me out.
Best,
Zhanmiao Feng
Hello,
thank you for providing this excellent tool, but I encountered some unexpected errors while running it. My Nextflow pipeline only executed the first six steps, then skipped the remaining steps and stopped without showing any errors. Do you have any idea what might be causing this issue?
Below is my output.
Below is my input.
Below is the content of my samples.tsv file.
Below is the content of my barcodes.tsv file.
I would be very grateful if you could take some time to help me out.
Best,
Zhanmiao Feng