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GuoliangLi-HZAU / BatMeth2

BS-seq analysis pipeline
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problem on methyGff! #4

Open cheehowteo opened 5 years ago

cheehowteo commented 5 years ago

Dear Prof. Qiangwei,

Good day!

I tried to run your BatMeth2 on Arabidopsis thaliana reads from NCBI SRA database as test run for the program. I used TAIR10.1 as reference and TAIR10.1.gff as annotation file. However, the BatMeth2 program only finished halfway.

I received several error messages as below:

  1. samtools sort -@ 4 -o ./SRR8100591_bathmeth2.sort.bam ./SRR8100591_bathmeth2.sam >> ./SRR8100591_bathmeth2.run.log 2>&1 [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped

  2. /home/user/Downloads/BatMeth2/bin/methyGff -o ./SRR8100591_bathmeth2 -G /mnt/D/Liaw/WGS-Bi/arabidopsis/Arabidopsis_thaliana/TAIR10.1/GCF_000001735.4_TAIR10.1_genomic.fa -gff /mnt/D/Liaw/WGS-Bi/arabidopsis/Arabidopsis_thaliana/TAIR10.1/GCF_000001735.4_TAIR10.1_genomic.gff -m ./SRR8100591_bathmeth2.methratio.txt -B -P --TSS --TTS --GENE -s 0.025 >> ./SRR8100591_bathmeth2.run.log 2>&1 Segmentation fault (core dumped)

  3. Error in file(file, "rt") : cannot open the connection Calls: read.table -> file Execution halted elements.methylevel.Aver.OutFile: ./SRR8100591_bathmeth2.Methenrich.pdf

  4. Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file './SRR8100591_bathmeth2.AverMethylevel.1.txt': No such file or directory Execution halted Rscript /home/user/Downloads/BatMeth2/bin/density_plot_with_methyl_oneSample_oneGff.r ./SRR8100591_bathmeth2.methBins.txt ./SRR8100591_bathmeth2.annoDensity.1.txt ./SRR8100591_bathmeth2.density.pdf SRR8100591_bathmeth2 >> ./SRR8100591_bathmeth2.run.log 2>&1

  5. 260910011469183923772383Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file './SRR8100591_bathmeth2.annoDensity.1.txt': No such file or directory Execution halted

  6. BatMeth2: mC Usage: Rscript thisRfile Inputfile1(mCdensity) OutFile1.pdf Inputfile2(mCcatero) OutFile2.pdf Warning message: In read.table(Infile, row.names = 1) : incomplete final line found by readTableHeader on './SRR8100591_bathmeth2.mCdensity.txt' null device 1 null device 1 null device 1 null device 1

  7. Usage: GeneMethHeatmap sample1 sample2[None] CG-ceil CHG-ceil CHH-ceil ./SRR8100591_bathmeth2 sort: cannot read: ./SRR8100591_bathmeth2.TSS.cg.1.txt: No such file or directory sort: cannot read: ./SRR8100591_bathmeth2.TTS.cg.1.txt: No such file or directory sort: cannot read: ./SRR8100591_bathmeth2.TSS.chg.1.txt: No such file or directory sort: cannot read: ./SRR8100591_bathmeth2.TTS.chg.1.txt: No such file or directory sort: cannot read: ./SRR8100591_bathmeth2.TSS.chh.1.txt: No such file or directory sort: cannot read: ./SRR8100591_bathmeth2.TTS.chh.1.txt: No such file or directory

  8. heatmap Loading required package: pheatmap [1] "Package pheatmap is loaded correctly" Error in read.table(paste(args[1], ".cg", sep = ""), sep = "\t") : no lines available in input Execution halted

May I know what is the problem causing these errors? and how can I fix these problem?

Thank you.

Best regards, Teo

GuoliangLi-HZAU commented 5 years ago

Could you provide information about genome and annotation files (download links, etc.)? Other error messages are due to methyGff's failure.

cheehowteo commented 5 years ago

Dear Prof. Guoliang, the genome that I used is Arabidopsis thaliana TAIR10.1 (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.4_TAIR10.1/GCF_000001735.4_TAIR10.1_genomic.fna.gz) and annotation file is GCF_000001735.4_TAIR10.1_genomic.gff.gz. For the sra file, I download it from NCBI SRA repository: SRR8100584.sra. Thank you. Best regards, Teo

GuoliangLi-HZAU commented 5 years ago

Hi Teo, We tested the data and did not report any errors. Can you follow the command to see what happen?

  1. ulimit-c unlimited
  2. run your Gff command A core file will be generated in your directory
  3. gdb /loaction/to/your/methGff core
  4. type BT

Then show us the information displayed. Or you can try downloading the current version and testing methyGff separately. / Home/user/Downloads/BatMeth2/bin/methyGff-o. /SRR8100591_bathmeth2-G/mnt/D/Liaw/WGS-Bi/arabidopsis/Arabidopsis_thaliana/TAIR 10.1/GCF_000001735.4_TAIR 10.1_genomic.fa-gff

Best Regards

cheehowteo commented 5 years ago

Dear Prof. Guoliang, I downloaded and try to do 'make' for the current version. But it failed. Here is the error messages:

make all-recursive make[1]: Entering directory '/home/user/Downloads/BatMeth2-master' Making all in src make[2]: Entering directory '/home/user/Downloads/BatMeth2-master/src' /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT adler32.o -MD -MP -MF .deps/adler32.Tpo -c -o adler32.o adler32.c mv -f .deps/adler32.Tpo .deps/adler32.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT compress.o -MD -MP -MF .deps/compress.Tpo -c -o compress.o compress.c mv -f .deps/compress.Tpo .deps/compress.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT crc32.o -MD -MP -MF .deps/crc32.Tpo -c -o crc32.o crc32.c mv -f .deps/crc32.Tpo .deps/crc32.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT gzio.o -MD -MP -MF .deps/gzio.Tpo -c -o gzio.o gzio.c mv -f .deps/gzio.Tpo .deps/gzio.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT uncompr.o -MD -MP -MF .deps/uncompr.Tpo -c -o uncompr.o uncompr.c mv -f .deps/uncompr.Tpo .deps/uncompr.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT deflate.o -MD -MP -MF .deps/deflate.Tpo -c -o deflate.o deflate.c mv -f .deps/deflate.Tpo .deps/deflate.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT trees.o -MD -MP -MF .deps/trees.Tpo -c -o trees.o trees.c mv -f .deps/trees.Tpo .deps/trees.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT zutil.o -MD -MP -MF .deps/zutil.Tpo -c -o zutil.o zutil.c mv -f .deps/zutil.Tpo .deps/zutil.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT inflate.o -MD -MP -MF .deps/inflate.Tpo -c -o inflate.o inflate.c mv -f .deps/inflate.Tpo .deps/inflate.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT infback.o -MD -MP -MF .deps/infback.Tpo -c -o infback.o infback.c mv -f .deps/infback.Tpo .deps/infback.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT inftrees.o -MD -MP -MF .deps/inftrees.Tpo -c -o inftrees.o inftrees.c mv -f .deps/inftrees.Tpo .deps/inftrees.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT inffast.o -MD -MP -MF .deps/inffast.Tpo -c -o inffast.o inffast.c mv -f .deps/inffast.Tpo .deps/inffast.Po rm -f libz.a ar cru libz.a adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o ar: u' modifier ignored sinceD' is the default (see `U') ranlib libz.a /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT bfix.o -MD -MP -MF .deps/bfix.Tpo -c -o bfix.o bfix.cpp mv -f .deps/bfix.Tpo .deps/bfix.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT index.o -MD -MP -MF .deps/index.Tpo -c -o index.o index.cpp mv -f .deps/index.Tpo .deps/index.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT BWT.o -MD -MP -MF .deps/BWT.Tpo -c -o BWT.o BWT.c mv -f .deps/BWT.Tpo .deps/BWT.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT MiscUtilities.o -MD -MP -MF .deps/MiscUtilities.Tpo -c -o MiscUtilities.o MiscUtilities.c mv -f .deps/MiscUtilities.Tpo .deps/MiscUtilities.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT MemManager.o -MD -MP -MF .deps/MemManager.Tpo -c -o MemManager.o MemManager.c mv -f .deps/MemManager.Tpo .deps/MemManager.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT TextConverter.o -MD -MP -MF .deps/TextConverter.Tpo -c -o TextConverter.o TextConverter.c mv -f .deps/TextConverter.Tpo .deps/TextConverter.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT r250.o -MD -MP -MF .deps/r250.Tpo -c -o r250.o r250.c mv -f .deps/r250.Tpo .deps/r250.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT QSufSort.o -MD -MP -MF .deps/QSufSort.Tpo -c -o QSufSort.o QSufSort.c mv -f .deps/QSufSort.Tpo .deps/QSufSort.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT iniparser.o -MD -MP -MF .deps/iniparser.Tpo -c -o iniparser.o iniparser.c mv -f .deps/iniparser.Tpo .deps/iniparser.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT inistrlib.o -MD -MP -MF .deps/inistrlib.Tpo -c -o inistrlib.o inistrlib.c mv -f .deps/inistrlib.Tpo .deps/inistrlib.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT dictionary.o -MD -MP -MF .deps/dictionary.Tpo -c -o dictionary.o dictionary.c mv -f .deps/dictionary.Tpo .deps/dictionary.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT DNACount.o -MD -MP -MF .deps/DNACount.Tpo -c -o DNACount.o DNACount.c mv -f .deps/DNACount.Tpo .deps/DNACount.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT Timing.o -MD -MP -MF .deps/Timing.Tpo -c -o Timing.o Timing.c mv -f .deps/Timing.Tpo .deps/Timing.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT Socket.o -MD -MP -MF .deps/Socket.Tpo -c -o Socket.o Socket.c mv -f .deps/Socket.Tpo .deps/Socket.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT HSP.o -MD -MP -MF .deps/HSP.Tpo -c -o HSP.o HSP.c mv -f .deps/HSP.Tpo .deps/HSP.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT HSPstatistic.o -MD -MP -MF .deps/HSPstatistic.Tpo -c -o HSPstatistic.o HSPstatistic.c mv -f .deps/HSPstatistic.Tpo .deps/HSPstatistic.Po /usr/local/bin/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -w -O3 -funroll-loops -maccumulate-outgoing-args -msse2 -lz -lm -pthread -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -MT karlin.o -MD -MP -MF .deps/karlin.Tpo -c -o karlin.o karlin.c mv -f .deps/karlin.Tpo .deps/karlin.Po make[2]: No rule to make target '-lm', needed by 'batmethindex'. Stop. make[2]: Leaving directory '/home/user/Downloads/BatMeth2-master/src' make[1]: [Makefile:255: all-recursive] Error 1 make[1]: Leaving directory '/home/user/Downloads/BatMeth2-master' make: *** [Makefile:193: all] Error 2

Thank you.

Best regards, Teo