Failed to create unitigs

[JETitus]

Hi,

I am not sure exactly what error is particularly occurring. However, I am not generating unitig.fa files at the end of my ABySS run. Attached is a text file with a whole run, start to error for one kmer = 71. The tail of the error is below.

AdjList    -k71 -m50 --dot raw_assembly/results/combined/combined_k71_cov_default-1.fa >raw_assembly/results/combined/combined_k71_cov_default-1.dot
abyss-filtergraph  --dot   -k71 -g raw_assembly/results/combined/combined_k71_cov_default-2.dot1 raw_assembly/results/combined/combined_k71_cov_default-1.dot raw_assembly/results/combined/combined_k71_cov_default-1.fa >raw_assembly/results/combined/combined_k71_cov_default-1.path
MergeContigs   -k71 -g raw_assembly/results/combined/combined_k71_cov_default-2.dot -o raw_assembly/results/combined/combined_k71_cov_default-2.fa raw_assembly/results/combined/combined_k71_cov_default-1.fa raw_assembly/results/combined/combined_k71_cov_default-2.dot1 raw_assembly/results/combined/combined_k71_cov_default-1.path
PopBubbles  --dot -j8 -k71  -p0.9  -g raw_assembly/results/combined/combined_k71_cov_default-3.dot raw_assembly/results/combined/combined_k71_cov_default-2.fa raw_assembly/results/combined/combined_k71_cov_default-2.dot >raw_assembly/results/combined/combined_k71_cov_default-2.path
MergeContigs   -k71 -o raw_assembly/results/combined/combined_k71_cov_default-3.fa raw_assembly/results/combined/combined_k71_cov_default-2.fa raw_assembly/results/combined/combined_k71_cov_default-2.dot raw_assembly/results/combined/combined_k71_cov_default-2.path
The minimum coverage of single-end contigs is 2.64583.
The minimum coverage of merged contigs is 2.65714.
Consider increasing the coverage threshold parameter, c, to 2.65714.
awk '!/^>/ {x[">" $1]=1; next} {getline s} $1 in x {print $0 "\n" s}' \
        raw_assembly/results/combined/combined_k71_cov_default-2.path raw_assembly/results/combined/combined_k71_cov_default-1.fa >raw_assembly/results/combined/combined_k71_cov_default-indel.fa
ln -sf raw_assembly/results/combined/combined_k71_cov_default-3.fa raw_assembly/results/combined/combined_k71_cov_default-unitigs.fa
ln: failed to create symbolic link ‘raw_assembly/results/combined/combined_k71_cov_default-unitigs.fa’: Function not implemented
make: *** [raw_assembly/results/combined/combined_k71_cov_default-unitigs.fa] Error 1

I am not sure if this an ABySS function, Linux issue the ln command, or what. From what I read the minimum coverage message is not an issue anymore since 1.3... From what I can see the issue is the ln command.

Below are the perl commands issued to ABySS through a perl script:

          system("abyss-pe mpirun=@{$mpi}[0] k=$k c=$cov e=$cov np=@{$np}[0] E=0 n=10 in=\'$file1 $file2\' se=$fileu name=$resultDir$lib\"_k\"$k\"_cov\"$cov  ");
      system("rm coverage.hist");

          system("abyss-pe mpirun=@{$mpi}[0] k=$k np=@{$np}[0] E=0 n=10 in=\'$file1 $file2\' se=$fileu name=$resultDir$lib\"_k\"$k\"_cov_default\"  ");
      system("rm coverage.hist");

Thank you for your time. If you need more information I can happily provide it.

Cheers, James script3_error_contigs.txt

[sjackman]

ln: failed to create symbolic link ‘…’: Function not implemented

Either your operating system or your file system does not support symbolic links. Which operating system are you using? Which file system are you using?

[JETitus]

I am running Bio Linux (Ubuntu kernel), which as far as I know and have found uses NFS filesystem.

I'll look more into it in the morning, but I found that Linux should support symbolic links. Hopefully that helps diagnose the problem.

Thank you for your time.

Cheers, James

[benvvalk]

Closing this issue due to staleness.