STAR Solo SmartSeq crashes with single-end data

[tzuni]

Using single-end SmartSeq data with STAR Solo results in an almost immediate crash.

I have tried with data originally generated as single-end and also one end of a paired end data set that otherwise works when used as paired-end data.

This is my command line, it works with paired-end data for me:

$STAR \
    --genomeDir ${star_idx} \
    --runThreadN 16 \
    --readFilesCommand zcat \
    --readFilesPrefix ${fastq_dir} \
    --readFilesManifest ${manifest} \
    --soloType SmartSeq \
    --soloFeatures Gene SJ GeneFull \
    --soloStrand Unstranded \
    --outSAMtype BAM Unsorted \
    --outSAMunmapped Within KeepPairs \
    --outSAMmultNmax 1

When I run this it will seg-fault and core dump without any error messages. The last output in Log.out file is the creation of the readsCommandsFile for the single-end data files (see attached).

Log_out.txt

[tzuni]

I wanted to add that my data manifest file has 2 columns in the single-end data, here's a few rows:

SRR6815583_1.fastq.gz   SRR6815583
SRR6815584_1.fastq.gz   SRR6815584
SRR6815585_1.fastq.gz   SRR6815585
SRR6815587_1.fastq.gz   SRR6815587
SRR6815588_1.fastq.gz   SRR6815588
SRR6815589_1.fastq.gz   SRR6815589
SRR6815591_1.fastq.gz   SRR6815591
SRR6815593_1.fastq.gz   SRR6815593
SRR6815595_1.fastq.gz   SRR6815595