no coverage in metawrap blobology picture

ucassee commented 5 years ago

Dear developer, I use metawrap blobology module to visualize the community. But all the plots are on the x-axis. I find the coverage of all contigs in file (final_assembly.blobplot) is 0. I just use the same command in the tutorial. So I wonder how can I modified it ? Thanks~

the following is error in the process

perl: symbol lookup error: /root/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Cwd/Cwd.so: undefined symbol: Perl_xs_apiversion_bootcheck
perl: symbol lookup error: /root/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Cwd/Cwd.so: undefined symbol: Perl_xs_apiversion_bootcheck
perl: symbol lookup error: /root/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Cwd/Cwd.so: undefined symbol: Perl_xs_apiversion_bootcheck
Mon Feb 18 13:41:16 2019 - Loading /data2017/share/tools/databases/NCBI_tax/nodes.dmp and /data2017/share/tools/databases/NCBI_tax/names.dmp into memory ...
Mon Feb 18 13:41:32 2019 - Loading /data2017/share/tools/databases/NCBI_tax/nodes.dmp and /data2017/share/tools/databases/NCBI_tax/names.dmp into memory ... DONE
Mon Feb 18 13:41:37 2019 - Loading assembly fasta file BLOBOLOGY/final_assembly.fasta into memory ...
Mon Feb 18 13:41:45 2019 - Loading assembly fasta file BLOBOLOGY/final_assembly.fasta into memory ... DONE
Mon Feb 18 13:41:45 2019 - Reading BLOBOLOGY/B10T1-19.bowtie2.bam ...
Mon Feb 18 13:41:45 2019 - Reading BLOBOLOGY/B10T1-19.bowtie2.bam ... DONE
Mon Feb 18 13:41:45 2019 - Reading BLOBOLOGY/B10T1-1.bowtie2.bam ...
Mon Feb 18 13:41:45 2019 - Reading BLOBOLOGY/B10T1-1.bowtie2.bam ... DONE
Mon Feb 18 13:41:46 2019 - Reading BLOBOLOGY/B10T1-23.bowtie2.bam ...
Mon Feb 18 13:41:46 2019 - Reading BLOBOLOGY/B10T1-23.bowtie2.bam ... DONE
Mon Feb 18 13:41:46 2019 - Making len gc cov taxon annotation data file BLOBOLOGY/final_assembly.fasta.txt for R ...
Mon Feb 18 13:41:48 2019 - Making len gc cov taxon annotation data file BLOBOLOGY/final_assembly.fasta.txt for R ... DONE
There were 14 warnings (use warnings() to see them)
There were 14 warnings (use warnings() to see them)
Warning messages:
1: Transformation introduced infinite values in continuous y-axis 
2: Transformation introduced infinite values in continuous y-axis 
3: Transformation introduced infinite values in continuous y-axis 
4: Transformation introduced infinite values in continuous y-axis 
5: Removed 32 rows containing missing values (geom_point). 
There were 48 warnings (use warnings() to see them)
Warning messages:
1: Transformation introduced infinite values in continuous y-axis 
2: Transformation introduced infinite values in continuous y-axis 
3: Removed 32 rows containing missing values (geom_point). 
There were 13 warnings (use warnings() to see them)
There were 46 warnings (use warnings() to see them)
There were 13 warnings (use warnings() to see them)
There were 13 warnings (use warnings() to see them)
Warning messages:
1: Transformation introduced infinite values in continuous y-axis 
2: Transformation introduced infinite values in continuous y-axis 
3: Transformation introduced infinite values in continuous y-axis 
4: Transformation introduced infinite values in continuous y-axis 

real    161m3.168s
user    4689m19.740s

ursky commented 5 years ago

Thats funny! Can you give me the first 10 lines of the .blobology file in the output directory? I want to see if its the plotting or data generation that produces this. Also, please provide the complete output of metawrap.

ucassee commented 5 years ago

Can you give me the first 10 lines of the .blobology file in the output directory?


seqid   len gc  cov_BLOBOLOGY/B10T1-19.bowtie2.bam  cov_BLOBOLOGY/B10T1-1.bowtie2.bam   cov_BLOBOLOGY/B10T1-23.bowtie2.bam  taxlevel_species    taxlevel_genus  taxlevel_family taxlevel_order  taxlevel_subclass   taxlevel_phylum taxlevel_superkingdom   bin binned_yes_no   binned_phylum
NODE_10009_length_4710_cov_17.529968    4710    0.677070063694267   0   0   0   Not annotated   Not annotated   Not annotated   Not annotated   Not annotated   Not annotated   Not annotated   bin.29.fa   Binned  Not annotated
NODE_1443_length_13759_cov_51.328444    13759   0.632386074569373   0   0   0   Azospirillum brasilense Azospirillum    Rhodospirillaceae   Rhodospirillales    Not annotated   Proteobacteria  Bacteria    bin.43.fa   Binned  Proteobacteria
NODE_1692_length_12543_cov_5.463085 12543   0.484971697361078   0   0   0   Sphingorhabdus flavimaris   Sphingorhabdus  Sphingomonadaceae   Sphingomonadales    Not annotated   Proteobacteria  Bacteria    bin.4.fa    Binned  Proteobacteria
NODE_57057_length_1906_cov_14.866018    1906    0.690451206715635   0   0   0   Magnetospirillum magneticum Magnetospirillum    Rhodospirillaceae   Rhodospirillales    Not annotated   Proteobacteria  Bacteria    bin.28.fa   Binned  Proteobacteria
NODE_30750_length_2625_cov_3.985214 2625    0.502095238095238   0   0   0   Not annotated   Not annotated   Not annotated   Not annotated   Not annotated   Not annotated   Not annotated   bin.47.fa   Binned  Not annotated
NODE_722_length_20072_cov_5.846730  20072   0.613690713431646   0   0   0   Deinococcus ficus   Deinococcus Deinococcaceae  Deinococcales   Not annotated   Deinococcus-Thermus Bacteria    bin.21.fa   Binned  Deinococcus-Thermus
NODE_2825_length_9353_cov_7.062702  9353    0.598724737922836   0   0   0   Dietzia sp. oral taxon 368  Dietzia Dietziaceae Corynebacteriales   Not annotated   Actinobacteria  Bacteria    bin.30.fa   Binned  Actinobacteria
NODE_67885_length_1743_cov_9.050355 1743    0.718301778542742   0   0   0   Nitrospirillum amazonense   Nitrospirillum  Rhodospirillaceae   Rhodospirillales    Not annotated   Proteobacteria  Bacteria    bin.28.fa   Binned  Proteobacteria
NODE_84089_length_1563_cov_12.968833    1563    0.72168905950096    0   0   0   Rhodospirillum centenum Rhodospirillum  Rhodospirillaceae   Rhodospirillales    Not annotated   Proteobacteria  Bacteria    bin.44.fa   Binned  Proteobacteria
NODE_11660_length_4358_cov_10.657216    4358    0.354290959155576   0   0   0   Not annotated   Not annotated   Not annotated   Not annotated   Not annotated   Not annotated   Not annotated   bin.5.fa    Binned  Not annotated

the output files contained in BLOBOLOGY are :

blobplot_figures blobplot_figures_only_binned_contigs final_assembly.binned.blobplot final_assembly.blobplot final_assembly.fasta final_assembly.fasta.1.bt2 final_assembly.fasta.2.bt2 final_assembly.fasta.3.bt2 final_assembly.fasta.4.bt2 final_assembly.fasta.rev.1.bt2 final_assembly.fasta.rev.2.bt2 final_assembly.nt.1e-5.megablast

ursky commented 5 years ago

Unfortunately, I am unable to replicate this issue. Can you check the contents of the .sam and .bam alignment files to see if the read alignment stage went ok? Also, having the complete metawrap output would be helpful.

ucassee commented 5 years ago

> 
perl: symbol lookup error: /root/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Cwd/Cwd.so: undefined symbol: Perl_xs_apiversion_bootcheck
perl: symbol lookup error: /root/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Cwd/Cwd.so: undefined symbol: Perl_xs_apiversion_bootcheck
perl: symbol lookup error: /root/perl5/lib/perl5/x86_64-linux-thread-multi/auto/Cwd/Cwd.so: undefined symbol: Perl_xs_apiversion_bootcheck

I resolve the issue and guess it result from the version of perl. The version of perl in metawrap-env is higher than original version. So, I can't call bowtie2 in metawrap-env. When I delete all environmental variable about perl in ~/.bashrc, bowtie2 can call in metawrap-env. I have another question. The concoct version in metawrap is 0.4.0, which is too slow. But the latest version of concoct (1.0.0) allows for high level of parallelisation. So I wonder whether I can update the concoct in metawrap?

ursky commented 5 years ago

Thats a good solution, I will try to remember it. For CONCOCT, thats a good point - i will look into adding v1.0 into metawrap as soon as I can in metawrap v1.1.4. For now, you can manually install concoct

bxlab / metaWRAP

no coverage in metawrap blobology picture #126