smoove exits with panic: exit status 1

[am8265]

Hello @brentp,

I ran smoove like this ---

smoove call --name ${sample} -x --exclude ${blist_region} --fasta ${FASTA} -p 3 --outdir ${sample}_smoove --genotype ${bam_path}

and the following logs were generated while running:

[smoove] 2021/12/28 07:01:59 starting with version 0.2.8
[smoove] 2021/12/28 07:01:59 calculating bam stats for 1 bams
[smoove] 2021/12/28 07:02:08 done calculating bam stats
[smoove]: ([E]lumpy-filter) 2021/12/28 07:18:36 [lumpy_filter] extracted splits and discordants from 998304035 total aligned reads
[smoove]:2021/12/28 07:19:13 finished process: lumpy-filter (set -eu; lumpy_filter -f /nfs/goldsteindata/refDB/HS_Build37/BWA_INDEX_hs37d5/hs37d5.fa /nfs/archive) in user-time:36m28.463383s system-time:2m31.014701s
could not load: libhts.so
compile with -d:nimDebugDlOpen for more information
panic: exit status 1

goroutine 24612 [running]:
github.com/brentp/smoove/lumpy.check(...)
        /home/brentp/src/smoove/lumpy/lumpy.go:54
github.com/brentp/smoove/lumpy.remove_sketchy(0xc0000224e0, 0x27, 0x3e8, 0x7fff26af12bf, 0x3e, 0x7fff26af126c, 0x4a, 0xc000188480, 0x4, 0x4, ...)
        /home/brentp/src/smoove/lumpy/depthfilter.go:232 +0x1825
github.com/brentp/smoove/lumpy.remove_sketchy_all.func1(0xc0000daa80, 0x3e8, 0x7fff26af12bf, 0x3e, 0x7fff26af126c, 0x4a, 0xc000188480, 0x4, 0x4, 0x1, ...)
        /home/brentp/src/smoove/lumpy/depthfilter.go:399 +0x231
created by github.com/brentp/smoove/lumpy.remove_sketchy_all
        /home/brentp/src/smoove/lumpy/depthfilter.go:397 +0x194
(base) dev1:LUMPY$ could not load: libhts.so
compile with -d:nimDebugDlOpen for more information

Is this has to do with loading library libhts.so?

Would really appreciate resolution to this issue and please let me know if you need more information.

Note: smoove generated these files successfully -- ${sample}.histo, ${sample}.disc.bam, ${sample}.split.bam (and *.split.bam.orig.bam and *disc.bam.orig.bam).

Thanks !

[brentp]

Hi, as you can see from the message, lumpy is not able to run because it is not able to find libhts.so. So this is a problem with your installation. How did you install smoove and associated dependencies?