Error running SoloTE v 1.09: FileNotFoundError: [Errno 2] No such file or directory: 'TN_allcounts.txt'

[t1nnenissen]

Hi there,

I have previously used this amazing tool and you have been a great help. I was really excited to realise the new features in the latest version that allows you to look at global levels of TE expression.

However, I ran into some difficulties running the new version. Please see below:

Do you have any idea as to what might cause this?

Best, Tinne

[bvaldebenitom]

Hi @t1nnenissen !

Thank you for the kind words.

Would you mind sharing the output of samtools view unassigned_alignments_prol.bam|head and ls -lht /Users/k20047529/Desktop/soloTE_v1.09/SoloTE_1.09/prol/TN_SoloTE_temp ?

[t1nnenissen]

Hi @bvaldebenitom,

Thank you so much for getting back on this!

For some reason the command would not run together:

However, it ran when I split into two:

It this hat you were looking for?

[bvaldebenitom]

Yes, that's it!

Can you try deleting the temporary folder and running again the pipeline? rm -Rf /Users/k20047529/Desktop/soloTE_v1.09/SoloTE_1.09/prol/TN_SoloTE_temp

python SoloTE_pipeline.py --threads 10 --bam unassigned_alignments_prol.bam --teannotation hg38_rmsk.bed --outputprefix TN --outputdir prol

Additionally, please share any messages from this new run. Also, share the output of head hg38_rmsk.bed samtools view -L hg38_rmsk.bed -c unassigned_alignments_prol.bam

[t1nnenissen]

After deleting the temporary folder and running the pipeline again I get this error:

head hg38_rmsk.bed output:

samtools view -L hg38_rmsk.bed -c unassigned_alignments_prol.bam output:

[bvaldebenitom]

It looks like the BAM file is missing the CB tag. What is the output of the following command? samtools view -c -e 'exists([CB])' unassigned_alignments_prol.bam

If you generated the BAM file using STAR, you can also report the command used to further confirm this.

[swainasish]

Yes, it was due to the "CB" tag, also don't forget to delete the existing dir I followed these parameters in the STAR STAR \ --runThreadN 60 \ --soloType Droplet \ --soloFeatures Gene \ --soloCBwhitelist $whitelist_adap \ --soloCBlen 16 \ --soloUMIstart 17 \ --soloUMIlen 10 \ --outSAMtype BAM SortedByCoordinate \ --twopassMode Basic \ --readFilesCommand zcat \ --outSAMattributes NH HI AS nM CR CY UR UY CB \ --outFilterMultimapNmax 100 \ --winAnchorMultimapNmax 100 \ --outSAMmultNmax 1 \ --genomeDir $genome_dir \ --readFilesIn SRR*_R2.fastq.gz SRR*_R1.fastq.gz

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