Open wcantara opened 4 years ago
shapemapper
commented
4 years ago Were you ever able to resolve this? First thing to check would be to make sure you installed from the release tarball and not by downloading the source only. If it still doesn't work, I'm curious what the output would be if you edit run_example.sh to add the flags "--verbose" and "--serial".
wcantara
commented
4 years ago Hello,
I installed from the release tarball at the link: https://github.com/Weeks-UNC/ShapeMapper2/releases/download/2.1.5/shapemapper-2.1.5.tar.gz
Here is the output when I use the "--verbose" and "--serial" flags: [wcantara@localhost shapemapper-2.1.5]$ ./run_example.sh
################################################################################################################################################################################
Started ShapeMapper v2.1.5 at 2020-03-10 14:50:38 Output will be logged to example-results_shapemapper_log.txt Running from directory: /home/wcantara/bin/shapemapper-2.1.5 args: --name example-results --target example_data/TPP.fa --amplicon --overwrite --verbose --serial --min-depth 1000 --modified --folder example_data/TPPplus --untreated --folder example_data/TPPminus --denatured --folder example_data/TPPdenat Created pipeline at 2020-03-10 14:50:38 Running PrimerLocator at 2020-03-10 14:50:38 . . .
python3 /home/wcantara/bin/shapemapper-2.1.5/internals/python/pyshapemap/locate_primers.py --fastas "example_data/TPP.fa" --primers-in-sequence --target-names "TPP" --locations-out "shapemapper_temp/example-results/PrimerLocator/example-results_PrimerLocator_locs_1.txt" --n-pairs-out "shapemapper_temp/example-results/PrimerLocator/example-results_PrimerLocator_n_pairs_1.txt"
from inside dir
/home/wcantara/bin/shapemapper-2.1.5
. . . done at 2020-03-10 14:50:39 Running FastaFormatChecker at 2020-03-10 14:50:39 . . .
python3 /home/wcantara/bin/shapemapper-2.1.5/internals/python/pyshapemap/../../bin/check_fasta_format.py "example_data/TPP.fa" "shapemapper_temp/example-results/AlignPrep/FastaFormatChecker/example-results_AlignPrep_FastaFormatChecker_corrected.fa"
from inside dir
/home/wcantara/bin/shapemapper-2.1.5
. . . done at 2020-03-10 14:50:39 Running BowtieIndexBuilder at 2020-03-10 14:50:39 . . .
bowtie2-build "example_data/TPP.fa" "shapemapper_temp/example-results/AlignPrep/BowtieIndexBuilder/example-results_AlignPrep_BowtieIndexBuilder_index"
from inside dir
/home/wcantara/bin/shapemapper-2.1.5
. . . done at 2020-03-10 14:50:39 Running Appender1 at 2020-03-10 14:50:39 . . .
cat "example_data/TPPplus/TPPplus_R1_aa.fastq.gz" "example_data/TPPplus/TPPplus_R1_ab.fastq.gz" "example_data/TPPplus/TPPplus_R1_ac.fastq.gz" "example_data/TPPplus/TPPplus_R1_ad.fastq.gz" > "shapemapper_temp/example-results/Modified/Appender1/example-results_Modified_Appender1_appended.fastq.gz"
from inside dir
/home/wcantara/bin/shapemapper-2.1.5
. . . done at 2020-03-10 14:50:39 Running Appender2 at 2020-03-10 14:50:39 . . .
cat "example_data/TPPplus/TPPplus_R2_aa.fastq.gz" "example_data/TPPplus/TPPplus_R2_ab.fastq.gz" "example_data/TPPplus/TPPplus_R2_ac.fastq.gz" "example_data/TPPplus/TPPplus_R2_ad.fastq.gz" > "shapemapper_temp/example-results/Modified/Appender2/example-results_Modified_Appender2_appended.fastq.gz"
from inside dir
/home/wcantara/bin/shapemapper-2.1.5
. . . done at 2020-03-10 14:50:40 Running ProgressMonitor at 2020-03-10 14:50:40 . . . . . . done at 2020-03-10 14:50:40 Running QualityTrimmer1 at 2020-03-10 14:50:40 . . .
shapemapper_read_trimmer -i "shapemapper_temp/example-results/Modified/ProgressMonitor/example-results_Modified_ProgressMonitor_output.fastq.gz" -o "shapemapper_temp/example-results/Modified/QualityTrimmer1/example-results_Modified_QualityTrimmer1_trimmed.fastq" -p "20" -l "25" -w "5"
from inside dir
/home/wcantara/bin/shapemapper-2.1.5
. . . done at 2020-03-10 14:50:40 Running QualityTrimmer2 at 2020-03-10 14:50:40 . . .
shapemapper_read_trimmer -i "shapemapper_temp/example-results/Modified/Appender2/example-results_Modified_Appender2_appended.fastq.gz" -o "shapemapper_temp/example-results/Modified/QualityTrimmer2/example-results_Modified_QualityTrimmer2_trimmed.fastq" -p "20" -l "25" -w "5"
from inside dir
/home/wcantara/bin/shapemapper-2.1.5
. . . done at 2020-03-10 14:50:40 Running Interleaver at 2020-03-10 14:50:40 . . .
python3 /home/wcantara/bin/shapemapper-2.1.5/internals/python/pyshapemap/../../bin/interleave_fastq.py "shapemapper_temp/example-results/Modified/QualityTrimmer1/example-results_Modified_QualityTrimmer1_trimmed.fastq" "shapemapper_temp/example-results/Modified/QualityTrimmer2/example-results_Modified_QualityTrimmer2_trimmed.fastq" "shapemapper_temp/example-results/Modified/Interleaver/example-results_Modified_Interleaver_interleaved.fastq"
from inside dir
/home/wcantara/bin/shapemapper-2.1.5
. . . done at 2020-03-10 14:50:41 Running Merger at 2020-03-10 14:50:41 . . .
bbmerge.sh vstrict=t in=stdin out=stdout outu=stdout interleaved=t usejni=t t=4 > "shapemapper_temp/example-results/Modified/Merger/example-results_Modified_Merger_output.fastq" < "shapemapper_temp/example-results/Modified/Interleaver/example-results_Modified_Interleaver_interleaved.fastq"
from inside dir
/home/wcantara/bin/shapemapper-2.1.5
| /``````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````````` | Merger (sample: Modified) output message: |
|---|---|
| java |
| -Djava.library.path=/home/wcantara/bin/shapemapper-2.1.5/internals/thirdparty/miniconda/opt/bbmap-37.78/jni/ -ea -Xmx1000m -Xmx1000m -cp /home/wcantara/bin/shapemapper-2.1.5/internals/thirdparty/miniconda/opt/bbmap-37.78/current/ jgi.BBMerge vstrict=t in=stdin out=stdout outu=stdout interleaved=t usejni=t t=4 | Executing jgi.BBMerge [vstrict=t, in=stdin, out=stdout, outu=stdout, interleaved=t, usejni=t, t=4] | Version 37.78 [vstrict=t, in=stdin, out=stdout, outu=stdout, interleaved=t, usejni=t, t=4] |
|---|---|---|
| Revised arguments: [maxbad=4, margin=3, minqo=8, qualiters=2, |
| ratiomode=t, flatmode=f, minentropy=52, minoverlap=12, minoverlap0=4, maxratio=0.05, ratiomargin=12, ratiooffset=0.5, ratiominoverlapreduction=4, efilter=2, pfilter=0.008, minsecondratio=0.16, minapproxoverlap=22, in=stdin, out=stdout, outu=stdout, interleaved=t, usejni=t, t=4] | Set INTERLEAVED to true | Set threads to 4 | Writing mergable reads merged. | Unspecified format for output stdout; defaulting to fastq. | Unspecified format for output stdout; defaulting to fastq. | Started output threads. | Unspecified format for input stdin; defaulting to fastq. | Total time: 0.361 seconds. | |
|---|---|---|---|---|---|---|---|---|---|
| Pairs: 8000 | |||||||||
| Joined: 2364 29.550% | |||||||||
| Ambiguous: 5635 70.438% | |||||||||
| No Solution: 1 0.013% | |||||||||
| Too Short: 0 0.000% | |||||||||
| Avg Insert: 134.7 | |||||||||
| Standard Deviation: 27.6 | |||||||||
| Mode: 146 | |||||||||
| Insert range: 40 - 209 | |||||||||
| 90th percentile: 146 | |||||||||
| 75th percentile: 146 | |||||||||
| 50th percentile: 145 | |||||||||
| 25th percentile: 143 | |||||||||
| 10th percentile: 94 |
___ . . . done at 2020-03-10 14:50:42 Running Tab6Interleaver at 2020-03-10 14:50:42 . . .
python3 /home/wcantara/bin/shapemapper-2.1.5/internals/python/pyshapemap/../../bin/tab6_interleave.py --input "shapemapper_temp/example-results/Modified/Merger/example-results_Modified_Merger_output.fastq" --output "shapemapper_temp/example-results/Modified/BowtieAlignerMixedInput/Tab6Interleaver/example-results_Modified_BowtieAlignerMixedInput_Tab6Interleaver_tab6.tab6"
from inside dir
/home/wcantara/bin/shapemapper-2.1.5
. . . done at 2020-03-10 14:50:42 Running BowtieAligner at 2020-03-10 14:50:42 . . .
bowtie2_wrapper.sh -p 4 --local --sensitive-local --mp 3,1 --rdg 5,1 --rfg 5,1 --dpad 30 --maxins 800 --ignore-quals --no-unal --tab6 - -x "shapemapper_temp/example-results/AlignPrep/BowtieIndexBuilder/example-results_AlignPrep_BowtieIndexBuilder_index" < "shapemapper_temp/example-results/Modified/BowtieAlignerMixedInput/Tab6Interleaver/example-results_Modified_BowtieAlignerMixedInput_Tab6Interleaver_tab6.tab6" -S "shapemapper_temp/example-results/Modified/BowtieAlignerMixedInput/BowtieAligner/example-results_Modified_BowtieAlignerMixedInput_BowtieAligner_aligned.sam"
from inside dir
/home/wcantara/bin/shapemapper-2.1.5
▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀▀ Component "BowtieAligner" (sample:Modified) status: failed (return code 127) ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── stdout ╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴ perl: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── stderr ╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴╴
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄ ShapeMapper run failed at 2020-03-10 14:50:44.
Any help you can provide would be most appreciated.
Cheers,
Will
Dr William Cantara, PhD
Research Scientist Department of Chemistry and Biochemistry, Center for RNA Biology and Center for Retrovirus Research The Ohio State University, Columbus, OH
On Wed, Mar 4, 2020 at 4:03 PM Steven Busan notifications@github.com wrote:
Were you ever able to resolve this? First thing to check would be to make sure you installed from the release tarball and not by downloading the source only. If it still doesn't work, I'm curious what the output would be if you edit run_example.sh to add the flags "--verbose" and "--serial".
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Weeks-UNC/shapemapper2/issues/12?email_source=notifications&email_token=AJPQSAWCFMOJIEOJSQMJTZ3RF26YVA5CNFSM4KJIORH2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEN2IOMY#issuecomment-594839347, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPQSAU6MT3D6KRQVO3HI53RF26YVANCNFSM4KJIORHQ .
shapemapper
commented
4 years ago Ugh. I overlooked that a number of bioconda executables (including Perl) attempt to dynamically link against system libraries, some of which are apparently missing or deprecated on systems like yours. I'm unlikely to fix this in my spare time in the near future.
Three possible solutions for you:
1) In your case, it seems likely that the system libnsl is a newer version (probably libnsl.so.2) than the version shapemapper's perl expects (libsnl.so.1). You may be able to quickly get things working by installing libnsl.so.1 alongside the newer version through your package manager (requires root privileges).
2) Alternatively, you could try creating a symbolic link in the appropriate lib directory named libsnl.so.1 that points to libsnl.so.2, but this has the potential to break your system if you do it incorrectly.
3) This option is the most time-consuming, but also the most likely to succeed in general. Delete the "shapemapper-2.1.5/internals/thirdparty" folder, and install all the required thirdparty packages listed in runtime dependencies at the system level. Some may be available through your package manager, but you may have to build others from source.
wcantara
commented
4 years ago Trust me; I'm very understanding of your frustrations. To help with any future requests, option 1 worked for me. The libnsl was available through the package manager, so it was a quick fix.
I did not try the other options, so I don't know if those would have worked.
Thanks for your help!
Cheers,
Will
Dr William Cantara, PhD
Research Scientist Department of Chemistry and Biochemistry, Center for RNA Biology and Center for Retrovirus Research The Ohio State University, Columbus, OH
On Tue, Mar 10, 2020 at 6:31 PM Steven Busan notifications@github.com wrote:
Ugh. I overlooked that a number of bioconda executables (including Perl) attempt to dynamically link against system libraries, some of which are apparently missing or deprecated on systems like yours. I'm unlikely to fix this in my spare time in the near future.
Three possible solutions for you:
1.
In your case, it seems likely that the system libnsl is a newer version (probably libnsl.so.2) than the version shapemapper's perl expects (libsnl.so.1). You may be able to quickly get things working by installing libnsl.so.1 alongside the newer version through your package manager (requires root privileges). 2.
Alternatively, you could try creating a symbolic link in the appropriate lib directory named libsnl.so.1 that points to libsnl.so.2, but this has the potential to break your system if you do it incorrectly. 3.
This option is the most time-consuming, but also the most likely to succeed in general. Delete the "shapemapper-2.1.5/internals/thirdparty" folder, and install all the required thirdparty packages listed in runtime dependencies https://github.com/Weeks-UNC/shapemapper2/blob/2.1.5/docs/building.md#runtime-dependencies at the system level. Some may be available through your package manager, but you may have to build others from source.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Weeks-UNC/shapemapper2/issues/12?email_source=notifications&email_token=AJPQSAVWJQPRISCIIVJ26FDRG25SRA5CNFSM4KJIORH2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEONOAPY#issuecomment-597352511, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPQSAXWNGL6QMJAHJHMDF3RG25SRANCNFSM4KJIORHQ .
After installation, my attempt at running the run_example.sh script hits a snag. Here is the error:
ERROR: Component "Tab6Interleaver" (sample:Modified) failed, giving the following error message: Traceback (most recent call last): File "/home/wcantara/bin/shapemapper-2.1.5/internals/python/pyshapemap/../../bin/tab6_interleave.py", line 70, in
o.write('\t'.join(fields) + '\n')
BrokenPipeError: [Errno 32] Broken pipe
I am running a fresh install of CentOS 8 (64-bit). Thanks!