Running and Verifying Abyss

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to decompress the test case package:

   tar xvf test-data.tar.gz

3. Run the following commands to switch the directory and perform the assembling:

   cd /path/to/TESTCASE
   abyss-pe k=25 name=test in='reads1.fastq reads2.fastq'

4. After the preceding steps are performed, only a single process can be executed. If multiple processes are executed, an error is reported, as shown in the following figure. To execute multiple processes concurrently, perform the following steps to modify the file.

   

   1. Run the following command to switch to the Abyss installation path and find the abyss-pe file:

      cd /path/to/ABYSS/bin

   2. Run the following command to modify the abyss-pe file:
      1. Open abyss-pe.

         vi abyss-pe

      2. Press i to enter the insert mode and add --allow-run-as-root -mca coll_hcoll_enable 0 to lines 543 and 551 of the abyss-pe file.

         $(gtime) $(mpirun) --allow-run-as-root -mca coll_hcoll_enable 0 -np $(np) abyss-paired-dbg-mpi $(abyssopt) $(ABYSS_OPTIONS) -o $*-1.fa $(in) $(se)
         $(gtime) $(mpirun) --allow-run-as-root -mca coll_hcoll_enable 0 -np $(np) ABYSS-P $(abyssopt) $(ABYSS_OPTIONS) -o $@ $(in) $(se)

      3. Press Esc, type :wq!, and press Enter to save the file and exit.
   3. Run the following command to switch the directory and perform the assembling:

      cd /path/to/TESTCASE/

      

      The name parameter indicates the prefix of the generated file. After the execution is complete, many files are generated, among which test-contigs.fa and test-scaffolds.fa correspond to the contig and scaffold results, respectively.

      The following command output is displayed:

      n       n:1000  L50     min     N80     N50     N20     E-size  max     sum     name
      756     19      6       1315    1752    3094    4947    3141    6122    47778   n=10 s=1000
      757     20      7       1315    1700    2214    4947    2991    6122    47778   n=10 s=2000
      759     22      9       1315    1700    2205    3191    2385    4066    47789   n=10 s=5000
      759     22      9       1315    1700    2205    3191    2385    4066    47789   n=10 s=10000
       
      Best scaffold N50 is 3094 at n=10 s=1000.
       
      n       n:1000  L50     min     N80     N50     N20     E-size  max     sum     name
      756     19      6       1315    1752    3094    4947    3141    6122    47778   n=10 s=1000
      PathConsensus  --dot -k25  -p0.9  -s test-7.fa -g test-7.dot -o test-7.path test-6.fa test-6.dot test-6.path
      Ambiguous paths: 3
      Merged:          0
      No paths:        3
      Too many paths:  0
      Too complex:     0
      Dissimilar:      0
      cat test-6.fa test-7.fa \
              |MergeContigs   -k25 -o test-8.fa - test-7.dot test-7.path
      The minimum coverage of single-end contigs is 2.28.
      The minimum coverage of merged contigs is 3.83248.
      Consider increasing the coverage threshold parameter, c, to 3.83248.
      ln -sf test-8.fa test-scaffolds.fa
      PathOverlap --overlap   -k25 --dot test-7.dot test-7.path >test-8.dot
      ln -sf test-8.dot test-scaffolds.dot
      abyss-fac   test-unitigs.fa test-contigs.fa test-scaffolds.fa |tee test-stats.tab
      n       n:500   L50     min     N80     N50     N20     E-size  max     sum     name