bvaldebenitom
commented
1 year ago Hi @frentzeperis !
Do you have a sub1-test_allcounts.txt file in /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/sub1-test_SoloTE_temp ? If so, please share the output of head sub1-test_allcounts.txt.
Additionally, can you share the output of the following commands?
ls -lht /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/sub1-test_SoloTE_temp
head /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/mm10_rmsk.bed
samtools view /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/possorted_genome_bam.bam|headThe output of those commands will help further diagnose these issues. Thanks!
frentzeperis
Good afternoon, I hope you are well!
I am using SoloTE 1.09 to analyze TE expression from a murine BAM file, it was aligned to mm10. I am trying to get the code running for the first subject before moving on to the others. It runs for a while but at the end got a few errors and the temp files were all still there. I would greatly appreciate any help!
Code: python SoloTE/SoloTE_pipeline.py --threads 1 --bam possorted_genome_bam.bam --teannotation mm10_rmsk.bed --outputprefix sub1-test --outputdir /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/
Output: SoloTE started at 12:28:50 [OK] samtools found! [OK] bedtools found! SoloTE v1.09 started! SoloTE Home directory /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/SoloTE SoloTE executed from /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te Results will be stored in /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te Input BAM file: /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/possorted_genome_bam.bam Input TE BED file: /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/mm10_rmsk.bed Currently working in temporary directory: /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/sub1-test_SoloTE_temp samtools view -@ 1 -O BAM -o sub1-test_nogenes_overlappingtes.bam -L /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/mm10_rmsk.bed -e '(exists([CB]) && exists([UB]) && [CB]!="-" && [UB]!="-") && (!exists([GN]) || [GN]=="-")' /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/possorted_genome_bam.bam samtools index sub1-test_nogenes_overlappingtes.bam sub1-test_nogenes_overlappingtes.bed exists in output folder. Skipping this step sub1-test_selectedtes.bed exists in output folder. Skipping this step python /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/SoloTE/annotateBAM.py sub1-test_nogenes_overlappingtes.bam sub1-test_selectedtes.bed temp_annotated_te.bam 1 samtools sort -@ 1 -O BAM -o sub1-test_teannotated.bam temp_annotated_te.bam samtools merge --threads 1 -o - /Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/possorted_genome_bam.bam sub1-test_teannotated.bam|samtools view -@ 1 -O BAM -o sub1-test_final.bam -e 'exists([CB]) && exists([UB]) && exists([GN]) && [CB]!="-" && [UB]!="-" && [GN]!="-"' --keep-tag GN,CB,UB samtools index sub1-test_final.bam Counts for chromosome chr1 are being generated in process: 19911 Counts for chromosome chr10 are being generated in process: 19911 Counts for chromosome chr11 are being generated in process: 19911 Counts for chromosome chr12 are being generated in process: 19911 Counts for chromosome chr13 are being generated in process: 19911 Counts for chromosome chr14 are being generated in process: 19911 Counts for chromosome chr15 are being generated in process: 19911 Counts for chromosome chr16 are being generated in process: 19911 Counts for chromosome chr17 are being generated in process: 19911 Counts for chromosome chr18 are being generated in process: 19911 Counts for chromosome chr19 are being generated in process: 19911 Counts for chromosome chr2 are being generated in process: 19911 Counts for chromosome chr3 are being generated in process: 19911 Counts for chromosome chr4 are being generated in process: 19911 Counts for chromosome chr5 are being generated in process: 19911 Counts for chromosome chr6 are being generated in process: 19911 Counts for chromosome chr7 are being generated in process: 19911 Counts for chromosome chr8 are being generated in process: 19911 Counts for chromosome chr9 are being generated in process: 19911 Counts for chromosome chrM are being generated in process: 19911 Counts for chromosome chrX are being generated in process: 19911 Counts for chromosome chrY are being generated in process: 19911 Counts for chromosome GL456233.1 are being generated in process: 19911 Counts for chromosome GL456211.1 are being generated in process: 19911 Counts for chromosome GL456350.1 are being generated in process: 19911 Counts for chromosome JH584293.1 are being generated in process: 19911 Counts for chromosome GL456221.1 are being generated in process: 19911 Counts for chromosome JH584297.1 are being generated in process: 19911 Counts for chromosome JH584296.1 are being generated in process: 19911 Counts for chromosome JH584294.1 are being generated in process: 19911 Counts for chromosome JH584298.1 are being generated in process: 19911 Counts for chromosome GL456210.1 are being generated in process: 19911 Counts for chromosome GL456212.1 are being generated in process: 19911 Counts for chromosome JH584304.1 are being generated in process: 19911 Counts for chromosome GL456216.1 are being generated in process: 19911 Counts for chromosome JH584295.1 are being generated in process: 19911 Traceback (most recent call last): File "/Users/frederikarentzeperis/opt/anaconda3/envs/soloTE/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3800, in get_loc return self._engine.get_loc(casted_key) File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 165, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 5745, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 5753, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 4
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/Users/frederikarentzeperis/Documents/Merad/2023-fall/test-te/SoloTE/SoloTE_pipeline.py", line 217, in
tecounts2.loc[tecounts2[4].isnull(),4] = tecounts2.loc[tecounts2[4].isnull(),1]
File "/Users/frederikarentzeperis/opt/anaconda3/envs/soloTE/lib/python3.9/site-packages/pandas/core/frame.py", line 3805, in getitem
indexer = self.columns.get_loc(key)
File "/Users/frederikarentzeperis/opt/anaconda3/envs/soloTE/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3802, in get_loc
raise KeyError(key) from err
KeyError: 4