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So I ran the souporcell without any common variants and inconsistent results when compared to the hashage information with cells with one hash being split into 3 cluster (attached) souporcell output https://drive.google.com/file/d/1JGWAGvx33oPItTh-d680kKlsrete2tdY/view?usp=sharing
Next, I tried running souporcell with common varaints and skip remap and this is what I get
checking modules imports done checking bam for expected tags checking fasta restarting pipeline in existing directory Ahmed_1GEXsnp using common variants 8 ***** WARNING: File Ahmed_1GEXsnp/depth_merged.bed has inconsistent naming convention for record: KI270727.1 20503 20713 ***** WARNING: File Ahmed_1GEXsnp/depth_merged.bed has inconsistent naming convention for record: KI270727.1 20503 20713 running vartrix running souporcell clustering /opt/souporcell/souporcell/target/release/souporcell -k 8 -a Ahmed_1GEXsnp/alt.mtx -r Ahmed_1GEXsnp/ref.mtx --restarts 100 -b /mnt/ravens/SequencingRuns/Tao/Ahmed1/sample_filtered_feature_bc_matrix/barcodes.tsv --min_ref 10 --min_alt 10 --threads 8 running souporcell doublet detection Traceback (most recent call last): File "/opt/souporcell/souporcell_pipeline.py", line 596, in <module> doublets(args, ref_mtx, alt_mtx, cluster_file) File "/opt/souporcell/souporcell_pipeline.py", line 541, in doublets subprocess.check_call([directory+"/troublet/target/release/troublet", "--alts", alt_mtx, "--refs", ref_mtx, "--clusters", cluster_file], stdout = dub, stderr = err) File "/usr/local/envs/py36/lib/python3.6/subprocess.py", line 311, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/opt/souporcell/troublet/target/release/troublet', '--alts', 'Ahmed_1GEXsnp/alt.mtx', '--refs', 'Ahmed_1GEXsnp/ref.mtx', '--clusters', 'Ahmed_1GEXsnp/clusters_tmp.tsv']' returned non-zero exit status 101.
this is the output I get souporcellouts.zip
The VCF file from the totourial did not work with me (download an empty file - attacehd) common_variants_grch38.zip So i used the file from https://www.dropbox.com/s/4nmm344g4j7pou4/GRCh38_1000G_MAF0.01_GeneFiltered_NoChr.vcf?e=4
I have around 6000 cells from 8 donors
The text was updated successfully, but these errors were encountered:
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So I ran the souporcell without any common variants and inconsistent results when compared to the hashage information with cells with one hash being split into 3 cluster (attached)
souporcell output https://drive.google.com/file/d/1JGWAGvx33oPItTh-d680kKlsrete2tdY/view?usp=sharing
Next, I tried running souporcell with common varaints and skip remap
and this is what I get
this is the output I get
souporcellouts.zip
The VCF file from the totourial did not work with me (download an empty file - attacehd)
common_variants_grch38.zip
So i used the file from https://www.dropbox.com/s/4nmm344g4j7pou4/GRCh38_1000G_MAF0.01_GeneFiltered_NoChr.vcf?e=4
I have around 6000 cells from 8 donors
The text was updated successfully, but these errors were encountered: