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.