lumpyexpress finishes without result

[arkyl]

Hi, I ran the following cmd: lumpyexpress -B ERR194147.bam -D ERR194147.bam.discordants.sort.bam -o output.vcf

The lumpyexpress finished within a few minutes without error message, but there is no output.vcf. I can run traditional lumpy and get a result. The bam has no split read info so only discordant pair bam was used. Any thought about this? Thanks very much.

[ryanlayer]

Does the BAM have read groups?

On Fri, Jun 22, 2018 at 3:59 PM ylark notifications@github.com wrote:

Hi, I ran the following cmd: lumpyexpress -B ERR194147.bam -D ERR194147.bam.discordants.sort.bam -o output.vcf

The lumpyexpress finished within a few minutes without error message, but there is no output.vcf. I can run traditional lumpy and get a result. The bam has no split read info so only discordant pair bam was used. Any thought about this? Thanks very much.

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[arkyl]

Yes. @RG ID:ERR194147_0 LB:ERR194147 PU:0 SM:ERR194147 Thanks for the fast reply.

[ryanlayer]

Can you paste in the output from lumpyexpress?

On Fri, Jun 22, 2018 at 4:13 PM ylark notifications@github.com wrote:

Yes. @rg https://github.com/rg ID:ERR194147_0 LB:ERR194147 PU:0 SM:ERR194147 Thanks for the fast reply.

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[arkyl]

Hi, Here is the output:

Sourcing executables from /home/liuy/software_installed/lumpy-sv/scripts/lumpyexpress.config ...

Checking for required python modules (/usr/bin/python)... Calculating insert distributions... Library read groups: ERR194147_0 Library read length: 101 Removed 77 outliers with isize >= 781 done

It stays at line "Library read length: 101" for a few minutes. Then stderr "Removed 77 outliers with isize >= 781" and "done". But no output.vcf.

Thanks much.

[ryanlayer]

Can you rerun with "-v" to get more output?

On Fri, Jun 22, 2018 at 4:36 PM ylark notifications@github.com wrote:

Hi, Here is the output:

Sourcing executables from /home/liuy/software_installed/lumpy-sv/scripts/lumpyexpress.config ...

Checking for required python modules (/usr/bin/python)... Calculating insert distributions... Library read groups: ERR194147_0 Library read length: 101 Removed 77 outliers with isize >= 781 done

It stays at line "Library read length: 101" for a few minutes. Then stderr "Removed 77 outliers with isize >= 781" and "done". But no output.vcf.

Thanks much.

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[arkyl]

Hi, I reran with -v (lumpyexpress -v -B ERR194147.bam -D ERR194147.bam.discordants.sort.bam -o output.vcf), but still get the same result:

Sourcing executables from /home/liuy/software_installed/lumpy-sv/scripts/lumpyexpress.config ...

Checking for required python modules (/usr/bin/python)...

create temporary directory

Calculating insert distributions... Library read groups: ERR194147_0 Library read length: 101 Removed 77 outliers with isize >= 781 done

[carleshf]

The same problem happened here:

lumpyexpress -v \
>     -B DN_bwa_b38_recal_leftalignindels_chr22.bam \
>     -S DN_bwa_b38_recal_leftalignindels_chr22.splitters.bam \
>     -D DN_bwa_b38_recal_leftalignindels_chr22.discordants.bam \
>     -o DN_bwa_b38_recal_leftalignindels_chr22.lumpyexpress.vcf

I put some "echo"s into the code and found that the execution stops at the command used to fill "SPL_SAMPLE".

SPL_SAMPLE=`$SAMT view -H $SPL_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`

I tested the same call to lumpyexpress with WES samples and it worked properly, but with WGS samples it is not generating the output.

[carleshf]

I extract the command from the Perl source file and run it in shell:

$ samtools view -H DN_bwa_b38_recal_leftalignindels_chr22.splitters.bam | grep -m 1 "^@RG" | gawk -v i=0 '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'
DN

So, I do not see why the script is stopping while or after running the command. But the "echo" printing the content of "SPL_SAMPLE" I put after it is not shown.

[carleshf]

Using the version distributed with seepseq (lumpy-sv @ dd4bf97) solved the problem (once removed "check_sq=False” from bamlibs.py).

[SilenWang]

I'm using lumpy-sv v0.2.14a distibuted on bioconda. And when I run the following code, there were some error:

#### My code ####
SAMPLE=sample
BAM_PATH=/path/to/bam/file

lumpyexpress \
    -B ${BAM_PATH}/${SAMPLE}.bam \
    -S ${SAMPLE}.splitters.bam \
    -D ${SAMPLE}.discordants.bam \
    -o ${SAMPLE}.vcf

#### Output I got ####
Sourcing executables from /path/to/lumpyexpress.config ...

Checking for required python modules (/path/to/python)...
/path/to/lumpyexpress: line 15: -n: command not found
/path/to/lumpyexpress: line 16: [: ==: unary operator expected
Traceback (most recent call last):
  File "/path/to/lumpy-sv-0.2.14a-2/scripts/bamkit/bamlibs.py", line 79, in <module>
    sys.exit(main())
  File "/path/to/lumpy-sv-0.2.14a-2/scripts/bamkit/bamlibs.py", line 74, in main
    get_libs(args.input, args.is_sam, True)
  File "/path/to/lumpy-sv-0.2.14a-2/scripts/bamkit/bamlibs.py", line 44, in get_libs
    in_bam = pysam.Samfile(bam, 'rb', check_sq=False)
  File "csamtools.pyx", line 463, in csamtools.Samfile.__cinit__ (pysam/csamtools.c:4758)
  File "csamtools.pyx", line 476, in csamtools.Samfile._open (pysam/csamtools.c:5052)
TypeError: _open() got an unexpected keyword argument 'check_sq'

I solved the first error in lumpyexpress line 15 & 16 by adding the following line to lumpyexpress.config

HEXDUMP=`which hexdump || true`

And the TypeError was solved accoding to @carleshf 's reply.

[ryanlayer]

Can you rerun with those fixes and send the new error?

On Oct 23, 2018, at 2:44 AM, SilenWang notifications@github.com wrote:

I'm using lumpy-sv v0.2.14a distibuted on bioconda. And when I run the following code, there were some error:

My code

SAMPLE=sample BAM_PATH=/path/to/bam/file

lumpyexpress \ -B ${BAM_PATH}/${SAMPLE}.bam \ -S ${SAMPLE}.splitters.bam \ -D ${SAMPLE}.discordants.bam \ -o ${SAMPLE}.vcf

Output I got

Sourcing executables from /path/to/lumpyexpress.config ...

Checking for required python modules (/path/to/python)... /path/to/lumpyexpress: line 15: -n: command not found /path/to/lumpyexpress: line 16: [: ==: unary operator expected Traceback (most recent call last): File "/path/to/lumpy-sv-0.2.14a-2/scripts/bamkit/bamlibs.py", line 79, in sys.exit(main()) File "/path/to/lumpy-sv-0.2.14a-2/scripts/bamkit/bamlibs.py", line 74, in main get_libs(args.input, args.is_sam, True) File "/path/to/lumpy-sv-0.2.14a-2/scripts/bamkit/bamlibs.py", line 44, in get_libs in_bam = pysam.Samfile(bam, 'rb', check_sq=False) File "csamtools.pyx", line 463, in csamtools.Samfile.cinit (pysam/csamtools.c:4758) File "csamtools.pyx", line 476, in csamtools.Samfile._open (pysam/csamtools.c:5052) TypeError: _open() got an unexpected keyword argument 'check_sq' I solved the first error in lumpyexpress line 15 & 16 by adding the following line to lumpyexpress.config

HEXDUMP=which hexdump || true And the TypeError was solved accoding to @carleshf 's reply.

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[SilenWang]

Emmmm, now lumpyexpress run without any problem, and the result seems to be fine.

Can you rerun with those fixes and send the new error? … On Oct 23, 2018, at 2:44 AM, SilenWang @.***> wrote: I'm using lumpy-sv v0.2.14a distibuted on bioconda. And when I run the following code, there were some error: #### My code #### SAMPLE=sample BAM_PATH=/path/to/bam/file lumpyexpress \ -B ${BAM_PATH}/${SAMPLE}.bam \ -S ${SAMPLE}.splitters.bam \ -D ${SAMPLE}.discordants.bam \ -o ${SAMPLE}.vcf #### Output I got #### Sourcing executables from /path/to/lumpyexpress.config ... Checking for required python modules (/path/to/python)... /path/to/lumpyexpress: line 15: -n: command not found /path/to/lumpyexpress: line 16: [: ==: unary operator expected Traceback (most recent call last): File "/path/to/lumpy-sv-0.2.14a-2/scripts/bamkit/bamlibs.py", line 79, in sys.exit(main()) File "/path/to/lumpy-sv-0.2.14a-2/scripts/bamkit/bamlibs.py", line 74, in main get_libs(args.input, args.is_sam, True) File "/path/to/lumpy-sv-0.2.14a-2/scripts/bamkit/bamlibs.py", line 44, in get_libs in_bam = pysam.Samfile(bam, 'rb', check_sq=False) File "csamtools.pyx", line 463, in csamtools.Samfile.cinit (pysam/csamtools.c:4758) File "csamtools.pyx", line 476, in csamtools.Samfile._open (pysam/csamtools.c:5052) TypeError: _open() got an unexpected keyword argument 'check_sq' I solved the first error in lumpyexpress line 15 & 16 by adding the following line to lumpyexpress.config HEXDUMP=which hexdump || true And the TypeError was solved accoding to @carleshf 's reply. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.