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smithlabcode / ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data
http://doi.org/djv4
GNU General Public License v3.0
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Error while processing the Ribo-Seq data using transcriptome based index #93

Closed HiteshKore closed 2 years ago

HiteshKore commented 2 years ago

Hi @saketkc,

I tried to analyze the bam file generated by mapping the ribosome footprints to transcriptome reference. However, I am getting error while running the Ribotricer.

Steps followed- 1) Transcriptome index generation using STAR:

STAR --runThreadN 15 --runMode genomeGenerate --genomeDir ./gencode_transcripts/ --genomeFastaFiles gencode.v33.transcripts.fa --limitGenomeGenerateRAM 357335127648 --genomeSAindexNbases 13

2) Ribosomal footprints were aligned to transcriptome reference. STAR --runThreadN 8 --runMode alignReads --genomeDir ./STAR_merged_transcriptome_index/gencode_transcripts/ --readFilesIn SRR1585486.fastq --alignEndsType EndToEnd --outFileNamePrefix SRR1585486 --outFilterMismatchNmax 2 --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --twopassMode Basic

2) Ribotricer was used to predict actively translating transcripts

ribotricer detect-orfs --bam SRR1585486.bam --ribotricer_index ./Riboticer/RiboTricer_customDB_02262021.txt --prefix SRR1585486-RT --phase_score_cutoff 0.44 --read_lengths 27,28,29,30,31,32

I am getting the following error-

Oct 28 17:18:18 ..... started ribotricer detect-orfs Oct 28 17:18:18 ... started parsing ribotricer index file Oct 28 17:18:20 ... started inferring experimental design [E::idx_find_and_load] Could not retrieve index file for 'SRR1585486_riboAligned.sortedByCoord.out.bam' Oct 28 17:19:38 ... started reading bam file [E::idx_find_and_load] Could not retrieve index file for 'SRR1585486_riboAligned.sortedByCoord.out.bam' 0%| | 0/68162965 [00:00<?, ?reads/s][E::idx_find_and_load] Could not retrieve index file for 'SRR1585486_riboAligned.sortedByCoord.out.bam' Oct 28 17:22:21 ... started plotting read length distribution Oct 28 17:22:22 ... started calculating metagene profiles. This may take a long time...

Oct 28 17:25:31 ... started plotting metagene profiles Oct 28 17:25:31 ... started inferring P-site offsets Traceback (most recent call last): File "/software/ribotricer/Python-3.7.7-venv-20210111/bin/ribotricer", line 11, in load_entry_point('ribotricer==1.3.2', 'console_scripts', 'ribotricer')() File "/software/ribotricer/Python-3.7.7-venv-20210111/lib/python3.7/site-packages/click-7.1.2-py3.7.egg/click/core.py", line 829, in call return self.main(args, kwargs) File "/software/ribotricer/Python-3.7.7-venv-20210111/lib/python3.7/site-packages/click-7.1.2-py3.7.egg/click/core.py", line 782, in main rv = self.invoke(ctx) File "/software/ribotricer/Python-3.7.7-venv-20210111/lib/python3.7/site-packages/click-7.1.2-py3.7.egg/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/software/ribotricer/Python-3.7.7-venv-20210111/lib/python3.7/site-packages/click-7.1.2-py3.7.egg/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/software/ribotricer/Python-3.7.7-venv-20210111/lib/python3.7/site-packages/click-7.1.2-py3.7.egg/click/core.py", line 610, in invoke return callback(args, **kwargs) File "/software/ribotricer/Python-3.7.7-venv-20210111/lib/python3.7/site-packages/ribotricer-1.3.2-py3.7.egg/ribotricer/cli.py", line 255, in detect_orfs_cmd File "/software/ribotricer/Python-3.7.7-venv-20210111/lib/python3.7/site-packages/ribotricer-1.3.2-py3.7.egg/ribotricer/detect_orfs.py", line 443, in detect_orfs File "/software/ribotricer/Python-3.7.7-venv-20210111/lib/python3.7/site-packages/ribotricer-1.3.2-py3.7.egg/ribotricer/metagene.py", line 281, in align_metagenes File "<__array_function__ internals>", line 6, in correlate File "/software/ribotricer/Python-3.7.7-venv-20210111/lib/python3.7/site-packages/numpy-1.19.5-py3.7-linux-x86_64.egg/numpy/core/numeric.py", line 713, in correlate return multiarray.correlate2(a, v, mode) ValueError: first array argument cannot be empty

I appreciate your help in resolving this issue.

Thank you

Kind regards, Hitesh

saketkc commented 2 years ago

If you can share the ribotricer index file and the bam file, I can take a look. My email is schoudhary@nygenome.org.

HiteshKore commented 2 years ago

Hi @saketkc,

It's not required now. I was trying to generate the index based on transcript sequences and perform the periodicity analysis using Ribotricer which might not be compatible with Ribotricer.

Thanks for all your help. Kind regards, Hitesh