search

10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
Other
340 stars 91 forks source link

incompatible with all the chemistries #236

Closed ab4cp closed 7 months ago

ab4cp commented 7 months ago

Hi, I'm trying to use cellranger-7.2.0 on ubuntu to align some publicly available datasets to the standard reference human genome.

An example dataset are available here: https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-7316 this is for Sample4-f6d6073b-340f-4030-95c6-241b61b1172c

The file names were downloaded as Retina_Wong_scRNA_Sample4_R1 etc. I've reformatted to be compatible with cellranger and tried to guess the lane but no matter which L001 or L002 etc it doesn't make a difference on the ouptut.

File names used: Sample4_S1_L001_I1_001.fastq.gz Sample4_S1__L001_R2_001.fastq.gz Sample4_S1_L001_R1_001.fastq.gz

I get the same error every public dataset not just this one. It always seems that read2 median length = 0. I've previously used cellranger without having this issue.

Any help would be greatly appreciated.

$/cellranger count --id practice --transcriptome refdata-gex-GRCh38-2020-A --fastqs /data/srafiles/f6d6073b-340f-4030-95c6-241b61b1172c --sample Sample4 --expect-cells 10000 --localcores 40 --localmem 100

Martian Runtime - v4.0.11 Serving UI at http://rdl-b5qh9t.desktop.cloud.unimelb.edu.au:42955?auth=_2L3kcxyYcE7mzQP1Nehy2kTCj_9zB73HBqfCE2ChdI

Running preflight checks (please wait)... Checking sample info... Checking FASTQ folder... Checking reference... Checking reference_path (/data/apps/refdata-gex-GRCh38-2020-A) on rdl-b5qh9t.desktop.cloud.unimelb.edu.au... Checking optional arguments... mro: v4.0.11 mrp: v4.0.11 Anaconda: Python 3.10.11 numpy: 1.24.3 scipy: 1.10.1 pysam: 0.21.0 h5py: 3.6.0 pandas: 1.5.3 STAR: 2.7.2a samtools: samtools 1.16.1 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX 2023-11-12 02:32:25 [runtime] (run:local) ID.practice.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX.fork0.chnk0.main 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.CHECK_SINGLE_BEAM_MODE 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SANITIZE_MAP_CALLS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COMPUTE_CORRECTION_FACTOR 2023-11-12 02:32:25 [runtime] (run:local) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COMPUTE_CORRECTION_FACTOR.fork0.chnk0.main 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG 2023-11-12 02:32:25 [runtime] (run:local) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG.fork0.chnk0.main 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY 2023-11-12 02:32:25 [runtime] (run:local) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY.fork0.chnk0.main 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX 2023-11-12 02:32:25 [runtime] (run:local) ID.practice.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX.fork0.chnk0.main 2023-11-12 02:32:25 [runtime] (chunks_complete) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2023-11-12 02:32:25 [runtime] (chunks_complete) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COMPUTE_CORRECTION_FACTOR 2023-11-12 02:32:26 [runtime] (failed) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY

[error] Pipestance failed. Error log at: practice/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/chnk0-u022b4f9e89/_errors

Log message: The read lengths are incompatible with all the chemistries for Sample Sample4 in "/data/srafiles/f6d6073b-340f-4030-95c6-241b61b1172c".

The minimum read length for different chemistries are: SFRP - read1: 26, read2: 30, index1: 0 SC5P-R2 - read1: 26, read2: 25, index1: 0 SC5P-PE - read1: 81, read2: 25, index1: 0 SC3Pv1 - read1: 25, read2: 10, index1: 14 SC3Pv2 - read1: 26, read2: 25, index1: 0 SC3Pv3 - read1: 26, read2: 25, index1: 0 SC3Pv3LT - read1: 26, read2: 25, index1: 0 SC3Pv3HT - read1: 26, read2: 25, index1: 0

We expect that at least 50% of the reads exceed the minimum length.

ab4cp commented 7 months ago

Hi, I'm trying to use cellranger-7.2.0 on ubuntu to align some publicly available datasets to the standard reference human genome.

An example dataset are available here: https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-7316 this is for Sample4-f6d6073b-340f-4030-95c6-241b61b1172c

The file names were downloaded as Retina_Wong_scRNA_Sample4_R1 etc. I've reformatted to be compatible with cellranger and tried to guess the lane but no matter which L001 or L002 etc it doesn't make a difference on the ouptut.

File names used: Sample4_S1_L001_I1_001.fastq.gz Sample4_S1__L001_R2_001.fastq.gz Sample4_S1_L001_R1_001.fastq.gz

I get the same error every public dataset not just this one. It always seems that read2 median length = 0. I've previously used cellranger without having this issue.

Any help would be greatly appreciated.

$/cellranger count --id practice --transcriptome refdata-gex-GRCh38-2020-A --fastqs /data/srafiles/f6d6073b-340f-4030-95c6-241b61b1172c --sample Sample4 --expect-cells 10000 --localcores 40 --localmem 100

Martian Runtime - v4.0.11 Serving UI at http://rdl-b5qh9t.desktop.cloud.unimelb.edu.au:42955?auth=_2L3kcxyYcE7mzQP1Nehy2kTCj_9zB73HBqfCE2ChdI

Running preflight checks (please wait)... Checking sample info... Checking FASTQ folder... Checking reference... Checking reference_path (/data/apps/refdata-gex-GRCh38-2020-A) on rdl-b5qh9t.desktop.cloud.unimelb.edu.au... Checking optional arguments... mro: v4.0.11 mrp: v4.0.11 Anaconda: Python 3.10.11 numpy: 1.24.3 scipy: 1.10.1 pysam: 0.21.0 h5py: 3.6.0 pandas: 1.5.3 STAR: 2.7.2a samtools: samtools 1.16.1 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX 2023-11-12 02:32:25 [runtime] (run:local) ID.practice.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX.fork0.chnk0.main 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.CHECK_SINGLE_BEAM_MODE 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SANITIZE_MAP_CALLS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COMPUTE_CORRECTION_FACTOR 2023-11-12 02:32:25 [runtime] (run:local) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COMPUTE_CORRECTION_FACTOR.fork0.chnk0.main 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG 2023-11-12 02:32:25 [runtime] (run:local) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG.fork0.chnk0.main 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY 2023-11-12 02:32:25 [runtime] (run:local) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY.fork0.chnk0.main 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX 2023-11-12 02:32:25 [runtime] (run:local) ID.practice.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX.fork0.chnk0.main 2023-11-12 02:32:25 [runtime] (chunks_complete) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2023-11-12 02:32:25 [runtime] (ready) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2023-11-12 02:32:25 [runtime] (chunks_complete) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COMPUTE_CORRECTION_FACTOR 2023-11-12 02:32:26 [runtime] (failed) ID.practice.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY

[error] Pipestance failed. Error log at: practice/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/chnk0-u022b4f9e89/_errors

Log message: The read lengths are incompatible with all the chemistries for Sample Sample4 in "/data/srafiles/f6d6073b-340f-4030-95c6-241b61b1172c".

  • read1 median length = 26
  • read2 median length = 0
  • index1 median length = 8

The minimum read length for different chemistries are: SFRP - read1: 26, read2: 30, index1: 0 SC5P-R2 - read1: 26, read2: 25, index1: 0 SC5P-PE - read1: 81, read2: 25, index1: 0 SC3Pv1 - read1: 25, read2: 10, index1: 14 SC3Pv2 - read1: 26, read2: 25, index1: 0 SC3Pv3 - read1: 26, read2: 25, index1: 0 SC3Pv3LT - read1: 26, read2: 25, index1: 0 SC3Pv3HT - read1: 26, read2: 25, index1: 0

We expect that at least 50% of the reads exceed the minimum length.

ab4cp commented 7 months ago

Fixed this by removing an underscore from the R2 input file.