Issue running zUMIs pipeline on Smartseq3 data

Describe the bug Pipeline fails with following message when I am running it on SmartSeq3 data.

EXITING: FATAL INPUT ERROR: empty value for parameter "readFilesIn" in input "Command-Line" SOLUTION: use non-empty value for this parameter

To Reproduce

project: HIV_umi_110121 sequence_files: file1: name: /hpcdata/vpds/current/Projects/HIV/HIV_UMI/reads_for_zUMIs.R1.fastq.gz base_definition:

cDNA(23-100)
UMI(12-19) find_pattern: ATTGCGCAATG file2: name: /hpcdata/vpds/current/Projects/HIV/HIV_UMI/reads_for_zUMIs.R2.fastq.gz base_definition:
cDNA(1-100) file3: name: /hpcdata/vpds/current/Projects/HIV/HIV_UMI/reads_for_zUMIs.index.fastq.gz base_definition:
BC(1-8) reference: STAR_index: /hpcdata/vpds/reference_sets/GRCh38+GRCm39_104/STAR GTF_file: /hpcdata/vpds/reference_sets/GRCh38+GRCm39_104/GRCh38_GRCm39.gtf additional_STAR_params: '' additional_files: ~ out_dir: /hpcdata/vpds/current/Projects/HIV/HIV_UMI num_threads: 8 mem_limit: 0 filter_cutoffs: BC_filter: num_bases: 1 phred: 20 UMI_filter: num_bases: 1 phred: 20 barcodes: barcode_num: ~ barcode_file: /hpcdata/vpds/current/Projects/HIV/HIV_UMI/reads_for_zUMIs.expected_barcodes.txt automatic: yes BarcodeBinning: 0 nReadsperCell: 100 counting_opts: introns: yes downsampling: '0' strand: 0 Ham_Dist: 0 velocyto: no primaryHit: yes twoPass: yes make_stats: yes which_Stage: Filtering samtools_exec: samtools pigz_exec: pigz STAR_exec: STAR Rscript_exec: Rscript zUMIs_directory: /nethome/current/zUMIs read_layout: PE

From runlog.txt You provided these parameters: YAML file: HIV_umi_110121.yaml zUMIs directory: /nethome/current/zUMIs STAR executable STAR samtools executable samtools pigz executable pigz Rscript executable Rscript RAM limit: 0 zUMIs version 2.9.7

[pm@ai-submit1 try2]$ cat HIV_umi_110121.filtered.tagged.Log.out STAR version=2.7.3a STAR compilation time,server,dir=Tue Oct 8 14:26:19 EDT 2019 vega:/home/dobin/data/STAR/STARcode/STAR.master/source

Command Line:

STAR --readFilesCommand samtools view -@ 1 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --genomeDir /hpcdata/vpds/reference_sets/GRCh38+GRCm39_104/STAR --sjdbGTFfile /hpcdata/vpds/reference_sets/GRCh38+GRCm39_104/GRCh38_GRCm39.gtf --runThreadN 7 --sjdbOverhang NA --readFilesType SAM PE --twopassMode Basic --readFilesIn --outFileNamePrefix /hpcdata/vpds/current/Projects/HIV/HIV_UMI/HIV_umi_110121.filtered.tagged.

Initial USER parameters from Command Line:

outFileNamePrefix /hpcdata/vpds/current/Projects/HIV/HIV_UMI/HIV_umi_110121.filtered.tagged.

All USER parameters from Command Line:

readFilesCommand samtools view -@ 1 ~RE-DEFINED outSAMmultNmax 1 ~RE-DEFINED outFilterMultimapNmax 50 ~RE-DEFINED outSAMunmapped Within ~RE-DEFINED outSAMtype BAM Unsorted ~RE-DEFINED quantMode TranscriptomeSAM ~RE-DEFINED genomeDir /hpcdata/vpds/reference_sets/GRCh38+GRCm39_104/STAR ~RE-DEFINED sjdbGTFfile /hpcdata/vpds/reference_sets/GRCh38+GRCm39_104/GRCh38_GRCm39.gtf ~RE-DEFINED runThreadN 7 ~RE-DEFINED sjdbOverhang 0 ~RE-DEFINED readFilesType SAM PE ~RE-DEFINED twopassMode Basic ~RE-DEFINED

EXITING: FATAL INPUT ERROR: empty value for parameter "readFilesIn" in input "Command-Line" SOLUTION: use non-empty value for this parameter

Nov 02 16:37:13 ...... FATAL ERROR, exiting Desktop (please complete the following information): HPC linux cluster (Red Hat Enterprise 7)

Additional context Pipeline runs fine with the example data

sdparekh / zUMIs