salmon: error while loading shared libraries: liblzma.so.0

[jiali0411]

Hi, I keep getting this error when running lorean with a genome of 580 Mb and ~240 G short read RNASeq data. I ran it in a singularity container. I also tried your Crispa example dataset, and it worked perfect but with a larger dataset, it always breaks at the Trinity step.
Here is the error:

) at /opt/LoReAn/third_party/software/Trinity/util/support_scripts/../../Trinity line 3866.
warning, cmd: /opt/LoReAn/third_party/software/Trinity/util/support_scripts/../../Trinity --single "Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq10/2/1807347_1808210.trinity.reads" --output "Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq10/2/1807347_1808210.trinity.reads.out" --CPU 1 --max_memory 3G --seqType fa --trinity_complete --full_cleanup --no_path_merging --max_reads_per_graph 100000   failed with ret: 32512, going to retry.
Error, cannot determine salmon version installed from (salmon: error while loading shared libraries: liblzma.so.0: cannot open shared object file: No such file or directory
succeeded(0), failed(78853)   100% completed.

We are sorry, commands in file: [FailedCommands] failed.  :-(

Error, cmd: /opt/LoReAn/third_party/software/Trinity/trinity-plugins/BIN/ParaFly -c trinity_GG.cmds -CPU 8 -v -shuffle  died with ret 256 at /opt/LoReAn/third_party/software/Trinity/Trinity line 2745.
	main::process_cmd("/opt/LoReAn/third_party/software/Trinity/trinity-plugins/BIN/"...) called at /opt/LoReAn/third_party/software/Trinity/Trinity line 3414
	main::run_partitioned_cmds("trinity_GG.cmds") called at /opt/LoReAn/third_party/software/Trinity/Trinity line 3372
	main::run_genome_guided_Trinity() called at /opt/LoReAn/third_party/software/Trinity/Trinity line 1367

I am using a server of 40 cores and 500G RAM. My command running lorean

singularity exec -B /path/to/wd/ -B /path/to/wd/Libraries/config/:/opt/LoReAn/third_party/software/augustus/config/ /path/to/LoReAn/lorean_latest.sif lorean \
-rp /path/to/repeatMask/genome.fasta.masked.out.gff \
-sr /path/to/raw_data/mRNA/all_1.fq,/path/to/raw_data/mRNA/all_2.fq \
-lr /path/to/raw_data/IsoSeq/all_Isoseq.fasta \
-pr /path/to/proteins.fasta \
-sp dar \
/path/to/genome.fasta \
-d \
-t 16 \
--keep_tmp &

Any suggestions or solutions?

Thanks,
Jiali

[jiali0411]

I looked at the trinity.log file and find the first time when the error comes out is here

Monday, September 14, 2020: 20:05:50    CMD: /opt/LoReAn/third_party/software/Trinity/trinity-plugins/BIN/ParaFly -c trinity_GG.cmds -CPU 8 -v -shuffle
Number of Commands: 78853
Error, cannot determine salmon version installed from (salmon: error while loading shared libraries: liblzma.so.0: cannot open shared object file: No such file or directory
) at /opt/LoReAn/third_party/software/Trinity/util/support_scripts/../../Trinity line 3866.
Error, cannot determine salmon version installed from (salmon: error while loading shared libraries: liblzma.so.0: cannot open shared object file: No such file or directory
) at /opt/LoReAn/third_party/software/Trinity/util/support_scripts/../../Trinity line 3866.
Error, cannot determine salmon version installed from (salmon: error while loading shared libraries: liblzma.so.0: cannot open shared object file: No such file or directory
) at /opt/LoReAn/third_party/software/Trinity/util/support_scripts/../../Trinity line 3866.
Error, cannot determine salmon version installed from (salmon: error while loading shared libraries: liblzma.so.0: cannot open shared object file: No such file or directory
) at /opt/LoReAn/third_party/software/Trinity/util/support_scripts/../../Trinity line 3866.
Error, cannot determine salmon version installed from (salmon: error while loading shared libraries: liblzma.so.0: cannot open shared object file: No such file or directory
) at /opt/LoReAn/third_party/software/Trinity/util/support_scripts/../../Trinity line 3866.
Error, cannot determine salmon version installed from (salmon: error while loading shared libraries: liblzma.so.0: cannot open shared object file: No such file or directory
) at /opt/LoReAn/third_party/software/Trinity/util/support_scripts/../../Trinity line 3866.
Error, cannot determine salmon version installed from (salmon: error while loading shared libraries: liblzma.so.0: cannot open shared object file: No such file or directory
) at /opt/LoReAn/third_party/software/Trinity/util/support_scripts/../../Trinity line 3866.
Error, cannot determine salmon version installed from (salmon: error while loading shared libraries: liblzma.so.0: cannot open shared object file: No such file or directory
) at /opt/LoReAn/third_party/software/Trinity/util/support_scripts/../../Trinity line 3866.