nested renamer is not supported #28
Description
Hi
I am running starseqr on my samples and stuck in error.
starseqr.py -1 sample_1.fastq.gz -2 sample_2.fastq.gz -m 1 -p starseqr_test -t 50 -i STAR_FUSION_LIB/ref_genome.fa.star.idx/ -g genomic.gtf -r genomic.fa -vv
2021-06-22 10:13 - INFO - STAR-SEQR***
2021-06-22 10:13 - INFO - CMD = /home/nipgr/software/STAR-SEQR/myenv/bin/starseqr.py -1 sample_1.fastq.gz -2 sample_2.fastq.gz -m 1 -p starseqr_test -t 50 -i STAR_FUSION_LIB/ref_genome.fa.star.idx/ -g genomic.gtf -r genomic.fa -vv
2021-06-22 10:13 - INFO - STAR-SEQR_version = 0.6.7
2021-06-22 10:13 - INFO - Starting to work on sample: /home/nipgr/Documents/chickpea/starseqr_test
2021-06-22 10:13 - INFO - Found input: sample_1.fastq.gz
2021-06-22 10:13 - INFO - Found input: sample_2.fastq.gz
2021-06-22 10:13 - INFO - Found input: genomic.fa
2021-06-22 10:13 - INFO - Found input: genomic.gtf
2021-06-22 10:13 - INFO - Starting STAR Alignment
2021-06-22 10:13 - INFO - *STAR Command: STAR --readFilesIn sample_1.fastq.gz sample_2.fastq.gz --readFilesCommand zcat --runThreadN 50 --genomeDir STAR_FUSION_LIB/ref_genome.fa.star.idx --outFileNamePrefix starseqr_test_STAR-SEQR/starseqr_test. --chimScoreJunctionNonGTAG -1 --outSAMtype None --chimOutType Junctions SeparateSAMold --alignSJDBoverhangMin 5 --outFilterMultimapScoreRange 1 --outFilterMultimapNmax 5 --outMultimapperOrder Random --outSAMattributes NH HI AS nM --chimSegmentMin 10 --chimJunctionOverhangMin 10 --chimScoreMin 1 --chimScoreDropMax 30 --chimScoreSeparation 7 --chimSegmentReadGapMax 3 --chimFilter None --twopassMode None --alignSJstitchMismatchNmax 5 -1 5 5 --chimMainSegmentMultNmax 10
2021-06-22 10:14 - INFO - b'Jun 22 10:13:02 ..... started STAR run\nJun 22 10:13:02 ..... loading genome\nJun 22 10:13:04 ..... started mapping\nJun 22 10:14:37 ..... finished mapping\nJun 22 10:14:37 ..... finished successfully\n'
2021-06-22 10:14 - INFO - STAR Alignment Finished!
2021-06-22 10:14 - INFO - Importing junctions
2021-06-22 10:14 - INFO - Number of candidates removed due to Mitochondria filter: 0
2021-06-22 10:14 - INFO - Removing duplicate reads
2021-06-22 10:14 - INFO - Begin multiprocessing of function apply_cigar_overhang in a pool of 50 workers using map_async protocol
2021-06-22 10:14 - INFO - Ordering junctions
2021-06-22 10:14 - INFO - Normalizing junctions
2021-06-22 10:14 - INFO - Begin multiprocessing of function apply_normalize_jxns in a pool of 50 workers using map_async protocol
2021-06-22 10:14 - INFO - Getting gene strand and flipping info as necessary
2021-06-22 10:14 - INFO - Begin multiprocessing of function apply_jxn_strand in a pool of 50 workers using map_async protocol
2021-06-22 10:15 - INFO - Begin multiprocessing of function apply_flip_func in a pool of 50 workers using map_async protocol
2021-06-22 10:15 - INFO - Aggregating junctions
Traceback (most recent call last):
File "/home/user/software/STAR-SEQR/myenv/bin/starseqr.py", line 622, in
sys.exit(main())
File "/home/user/software/STAR-SEQR/myenv/bin/starseqr.py", line 345, in main
jxn_summary = su.core.count_jxns(jxns)
File "/home/user/software/STAR-SEQR/myenv/lib64/python3.6/site-packages/starseqr_utils/core.py", line 123, in count_jxns
col)), ('counts', 'count')])), ('overhang_len', 'max')])).reset_index()
File "/home/user/software/STAR-SEQR/myenv/lib64/python3.6/site-packages/pandas/core/groupby/generic.py", line 940, in aggregate
result, how = self._aggregate(func, *args, **kwargs)
File "/home/user/software/STAR-SEQR/myenv/lib64/python3.6/site-packages/pandas/core/base.py", line 351, in _aggregate
raise SpecificationError("nested renamer is not supported")
pandas.core.base.SpecificationError: nested renamer is not supported