Hi,
I am running the docker version of trinity and successfully assembled the transcriptome. All the results directed to "trinity_results" folder in my current working directory. I was also able to run Busco and SAM tools to generate the statistics on the assembly.
However, when I run the program "align_and_estimate_abundance.pl" (rsem or kallisto mode) there is no output directory. Although the log of the kallisto run shows abundance.tsv.genes file written to ES_rep1 folder. But I can't find any such folder in the current working directory.
Here is the command to run the above mentioned program:
docker run -vpwd:pwd trinityrnaseq/trinityrnaseq /usr/local/bin/trinityrnaseq/util/align_and_estimate_abundance.pl \
--transcripts pwd/trinity_results/Trinity.fasta --seqType fq \
--samples_file pwd/samples.txt --thread_count 15 --est_method kallisto --trinity_mode --prep_reference
I will highly appreciate if anyone could help me to figure out what's going wrong here. Thanks.
