'Exiting due to error in worker thread' and sorting sam file related issue

[kwonej0617]

Hi @EricKutschera , Thank you for developing a useful tool!

I have install espresso with conda environment. I run espresso with the provided test data and it was running well. I am in progress of running espresso with my data.

gtf='GRCh38.gtf' #annotation of isoforms
sample_info='espresso_data/input/sample_list.tsv'
ref_genome='hg38.fa' #reference sequence
output_path='espresso_data/HEK293T-rep1'

#step1
perl espresso_code/src/ESPRESSO_S.pl -A ${gtf} -L ${sample_info} -F ${ref_genome} -O ${output_path} -T 20

However, I encountered the following error message:

PLEASE NOTE: This is an experimental module to load a centrally installed
miniconda environment. We do not recommend using this to install your own conda
environments; we do recommend installing miniconda in your /pi space to do so. 
Thread 2 terminated abnormally: bam_minimap2/HEK293T_WT-rep1/HEK293T_WT-rep1.sam is not sorted at espresso_code/src/ESPRESSO_S.pl line 947, <IN> line 472.
Thread 1 terminated abnormally: bam_minimap2/HEK293T_KO-rep1/HEK293T_KO-rep1.sam is not sorted at espresso_code/src/ESPRESSO_S.pl line 947, <IN> line 473.
Exiting due to error in worker thread

Could you please help me how to solve this issue? Thank you for your time!

[kwonej0617]

I additionally run samtools sort after minimap2 alignment. With the sorted file, ESPRESSO_S.pl seems running well so far...

minimap2 -ax splice --splice-flank=no -w 4 -k 14 ${mmi} ${fastq} > HEK293T_WT-rep1.sam
samtools sort -o HEK293T_WT-rep1_sorted.sam HEK293T_WT-rep1.sam