lumpyexpress error

[assane-mbodj]

Hello I am new in programming and I wanted to test lumpy on my Arabodopsis data When I run lumpyexpress I get this error

$lumpyexpress -B file.sorte.bam -S file.splitters.sorted.bam -D file.discordants.sorted.bam -o file.vcf Sourcing executables from /usr/local/bin/lumpyexpress.config ...

Checking for required python modules (/home/assane/anaconda3/envs/hecaton_py2/bin/python)... Calculating insert distributions... /home/assane/anaconda3/envs/hecaton_py2/bin/samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory Library read groups: id Library read length: 0 /home/assane/anaconda3/envs/hecaton_py2/bin/samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory Usage: pairend_distro.py [options]

pairend_distro.py: error: Read length not given Traceback (most recent call last): File "/home/assane/lumpy-sv//scripts/bamkit/bamfilterrg.py", line 127, in sys.exit(main()) File "/home/assane/lumpy-sv//scripts/bamkit/bamfilterrg.py", line 123, in main bamfilterrg(args.input, args.readgroup, args.n, args.S, args.b, args.u) File "/home/assane/lumpy-sv//scripts/bamkit/bamfilterrg.py", line 24, in bamfilterrg in_bam = pysam.Samfile('-', 'rb') File "pysam/libcalignmentfile.pyx", line 742, in pysam.libcalignmentfile.AlignmentFile.cinit File "pysam/libcalignmentfile.pyx", line 947, in pysam.libcalignmentfile.AlignmentFile._open ValueError: file does not contain alignment data

Can someone help me please

[ryanlayer]

Looks like an issues with your samtools. See

https://github.com/merenlab/anvio/issues/1479

On Fri, Apr 23, 2021 at 4:42 AM assane-mbodj @.***> wrote:

Hello I am new in programming and I wanted to test lumpy on my Arabodopsis data When I run lumpyexpress I get this error

$lumpyexpress -B file.sorte.bam -S file.splitters.sorted.bam -D file.discordants.sorted.bam -o file.vcf Sourcing executables from /usr/local/bin/lumpyexpress.config ...

Checking for required python modules (/home/assane/anaconda3/envs/hecaton_py2/bin/python)... Calculating insert distributions... /home/assane/anaconda3/envs/hecaton_py2/bin/samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory Library read groups: id Library read length: 0 /home/assane/anaconda3/envs/hecaton_py2/bin/samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory Usage: pairend_distro.py [options]

pairend_distro.py: error: Read length not given Traceback (most recent call last): File "/home/assane/lumpy-sv//scripts/bamkit/bamfilterrg.py", line 127, in sys.exit(main()) File "/home/assane/lumpy-sv//scripts/bamkit/bamfilterrg.py", line 123, in main bamfilterrg(args.input, args.readgroup, args.n, args.S, args.b, args.u) File "/home/assane/lumpy-sv//scripts/bamkit/bamfilterrg.py", line 24, in bamfilterrg in_bam = pysam.Samfile('-', 'rb') File "pysam/libcalignmentfile.pyx", line 742, in pysam.libcalignmentfile.AlignmentFile.cinit File "pysam/libcalignmentfile.pyx", line 947, in pysam.libcalignmentfile.AlignmentFile._open ValueError: file does not contain alignment data

Can someone help me please

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[assane-mbodj]

Hello

I want to test lumpy on two samples at the same time but it doesn't work. It doesn't find the indexed files even though I have them.

Here is the output

assane@gwas:~/lumpy-sv/output_PO10C$ lumpyexpress -B PO10A.sorted.bam,PO10C.sorted.bam -S PO10A.splitters.sorted.bam,PO10C.splitters.sorted.bam -D PO10A.discordants.sorted.bam,PO10C.discordants.sorted.bam -o multi_PO10.vcf Sourcing executables from /usr/local/bin/lumpyexpress.config ...

Checking for required python modules (/usr/bin/python)... Calculating insert distributions... Library read groups: id Library read length: 150 [E::idx_find_and_load] Could not retrieve index file for '-' Removed 1233 outliers with isize >= 924 done 1 Calculating insert distributions... Library read groups: id Library read length: 150 [E::idx_find_and_load] Could not retrieve index file for '-' Removed 1630 outliers with isize >= 1097 done 1 Running LUMPY... 697 0 Could not open input BAM files: BamMultiReader::Open: unable to open inconsistent files:
BamMultiReader::ValidateReaders: mismatched references found inPO10C.discordants.sorted.bamexpected: but found:

Thank you for your help

[yefanglee]

I met the same error as yours, I wonder did you solve it?

Could not open input BAM files: BamMultiReader::Open: unable to open all files:
unable to open file: data/LPY26.disc.bam unable to open file: data/LPY26.spli.bam unable to open file: data/LSD13.disc.bam unable to open file:data/LSD13.spli.bam