ValueError: Invalid Mode: uR

[Kiliankleemann]

Hello, I'm getting the following error:

INFO: Processing BAM/SAM files ...2024-04-12 11:37:02 Traceback (most recent call last): File "/home/kilian/miniconda3/bin/scTE", line 4, in import('pkg_resources').run_script('scTE==1.0', 'scTE') File "/home/kilian/miniconda3/lib/python3.11/site-packages/pkg_resources/init.py", line 722, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/kilian/miniconda3/lib/python3.11/site-packages/pkg_resources/init.py", line 1561, in run_script exec(code, namespace, namespace) File "/home/kilian/miniconda3/lib/python3.11/site-packages/scTE-1.0-py3.11.egg/EGG-INFO/scripts/scTE", line 173, in main() File "/home/kilian/miniconda3/lib/python3.11/site-packages/scTE-1.0-py3.11.egg/EGG-INFO/scripts/scTE", line 109, in main checkCBUMI(filename=k,out=outname,CB=args.CB,UMI=args.UMI) File "/home/kilian/miniconda3/lib/python3.11/site-packages/scTE-1.0-py3.11.egg/scTE/base.py", line 113, in checkCBUMI o=open('%s_scTEtmp/o1/testCR.txt'%(out),'rU') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: invalid mode: 'rU'

Not sure how to work around this - what I did wrong?

Please see my starSolo Script: mkdir Alignment_EM STAR --runMode alignReads \ --soloType Droplet \ --genomeDir /media/kilian/OS/STAR_index_hg38 \ --readFilesIn fastq_files/APOE1/APOE1_S1_L001_R2_001.fastq.gz,fastq_files/APOE1/APOE1_S1_L002_R2_001.fastq.gz,fastq_files/APOE1/APOE1_S1_L003_R2_001.fastq.gz \ fastq_files/APOE1/APOE1_S1_L001_R1_001.fastq.gz,fastq_files/APOE1/APOE1_S1_L002_R1_001.fastq.gz,fastq_files/APOE1/APOE1_S1_L003_R1_001.fastq.gz \ --soloCBwhitelist /media/kilian/OS/STAR_reference_files/3M-february-2018.txt \ --outSAMtype BAM Unsorted \ --outSAMattributes NH HI AS nM CR CY UR UY \ --readFilesCommand zcat \ --outFilterMultimapNmax 100 \ --winAnchorMultimapNmax 100 \ --outMultimapperOrder Random \ --runRNGseed 777 \ --outSAMmultNmax 1 \ --twopassMode Basic \ --soloUMIlen 10 \ --soloMultiMappers EM \ --runThreadN 16 \ --outFileNamePrefix Alignment_EM/APOE1_S1 \ --outReadsUnmapped Fastx \ --outSAMunmapped Within \ --soloBarcodeReadLength 0

And the alignment summary: Number of Reads,25400926 Reads With Valid Barcodes,0.980799 Sequencing Saturation,0.150308 Q30 Bases in CB+UMI,0.962055 Q30 Bases in RNA read,0.923963 Reads Mapped to Genome: Unique+Multiple,0.909326 Reads Mapped to Genome: Unique,0.797794 Reads Mapped to Gene: Unique+Multiple Gene,0.203119 Reads Mapped to Gene: Unique Gene,0.18643 Estimated Number of Cells,3893 Unique Reads in Cells Mapped to Gene,2640997 Fraction of Unique Reads in Cells,0.557703 Mean Reads per Cell,678 Median Reads per Cell,605 UMIs in Cells,2232977 Mean UMI per Cell,573 Median UMI per Cell,512 Mean Gene per Cell,329 Median Gene per Cell,292 Total Gene Detected,18279

I would greatly appreciate advice and help :)

[jphe]

The U file mode was removed in Python 3.11. I'll fix scTE later, you can run with python 3.10 or older

[jphe]

have fixed this problem, can you reinstall it and try again?

[Kiliankleemann]

Ill try today - Will let you know.