cziegenhain
commented
2 years ago Hi,
Please gzip your fastq files, plain fastq file mode is depreciated.
The rest should hopeful just be downstream errors. Best, C
27 juli 2022 kl. 09:15 skrev Lucas @.***>:
I am trying to run zUMI's on a SPLiT-seq dataset and several errors occur and no results are produced, I cannot figure out the source.
I have created a conda environment with all the recommended settings from the Wiki. Additionally i have tried running zUMIs in the provided conda channel with the '-c' option. Both provide the same result.
Below in the image you see the error messages that are produced while running zUMIs.
The script continues to run but produces errors at every step, most likely due to the fact that it goes wrong in the beginning.
The first error (sh: 1: Syntax error: Unterminated quoted string) i have localized to the fqfilter_v2.pl on line 92 $oriBase = basename $oriF'; When removing the ' from the script it removes that specific error but does not remove any of the errors below that.
When investigating the next error I am not sure whether something goes wrong and that is the cause of not finding the 'XC' object or that there is something wrong the XC object itself.
The YAML file i use is here:
project: zUMI_benchmark sequence_files: file1: name: /media/draco/lucask/AlgorithmTest/SRR6750041_1.fastq base_definition: (1-66) file2: name: /media/draco/lucask/AlgorithmTest/SRR6750041_2.fastq base_definition:
- BC(11-18,48-56,87-94)
- UMI(1-10) reference: STAR_index: /media/draco/lucask/genomes/mouse/M28_ALL/M28_ALL_STAR2-5-4/ GTF_file: /media/draco/lucask/genomes/mouse/M28_ALL/gencode.vM28.basic.annotation.gtf additional_STAR_params: '' additional_files: ~ out_dir: /media/draco/lucask/AlgorithmTest/zUMI/ 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: /media/draco/lucask/AlgorithmTest/zUMI/allBC_Whitelist.txt automatic: no BarcodeBinning: 2 nReadsperCell: 100 barcode_sharing: /media/draco/lucask/AlgorithmTest/zUMI/Shared_BC.txt counting_opts: introns: yes downsampling: '0' strand: 0 Ham_Dist: 1 velocyto: no primaryHit: yes twoPass: yes make_stats: yes which_Stage: Filtering Rscript_exec: Rscript STAR_exec: STAR pigz_exec: pigz samtools_exec: samtools
The whitelist consist of all of the possible barcode combinations from the SPLiT-seq protocol (~880k possibilities) and the Shared_BC.txt consist of the randHex and OligodT barcodes that should be paired formatted as described in the wiki.
I have used different STAR indexes, from both 2.5.4 (the recommended) as well as 2.7.10 (the latest).
I am not sure what i am doing wrong, maybe it is something simple that I am just missing, could you please help me.
Kind regards, Lucas Kuijpers
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LJK1991
without binning
Saying my .fasta file is wrong. I have used several other tools and aligners which had no problem with it at all.
Hopefully you can help.
I am trying to run zUMI's on a SPLiT-seq dataset and several errors occur and no results are produced, I cannot figure out the source.
I have created a conda environment with all the recommended settings from the Wiki. Additionally i have tried running zUMIs in the provided conda channel with the '-c' option. Both provide the same result.
Below in the image you see the error messages that are produced while running zUMIs.
The script continues to run but produces errors at every step, most likely due to the fact that it goes wrong in the beginning.
The first error (sh: 1: Syntax error: Unterminated quoted string) i have localized to the fqfilter_v2.pl on line 92 $oriBase =
basename $oriF'; When removing the ' from the script it removes that specific error but does not remove any of the errors below that.When investigating the next error I am not sure whether something goes wrong and that is the cause of not finding the 'XC' object or that there is something wrong the XC object itself.
The YAML file i use is here:
project: zUMI_benchmark sequence_files: file1: name: /media/draco/lucask/AlgorithmTest/SRR6750041_1.fastq base_definition: (1-66) file2: name: /media/draco/lucask/AlgorithmTest/SRR6750041_2.fastq base_definition:
The whitelist consist of all of the possible barcode combinations from the SPLiT-seq protocol (~880k possibilities) and the Shared_BC.txt consist of the randHex and OligodT barcodes that should be paired formatted as described in the wiki.
I have used different STAR indexes, from both 2.5.4 (the recommended) as well as 2.7.10 (the latest).
I am not sure what i am doing wrong, maybe it is something simple that I am just missing, could you please help me.
Kind regards, Lucas Kuijpers