Troubleshooting fastx-toolkit. Trying to resolve this error. I have uninstalled the newer versions of both libgtextutils and fastx_toolkit and am reverting to hopefully a more stable version. 

The "Abort trap: 6" was never really resolved for me but after running this version and compiling from source, the error does go away (can't say it is resolved). However, a new suite of errors with the older version pops up. Curiously, this is accounted for in the newer version. The errors are similar to the installation of phylobayes. I have troubleshooted them here and have a successful installation. Now hopefully I can move on with my life. I am going to try something new.

Anyways, here is the installation error workaround:

cd /usr/local/bin/
wget http://cancan.cshl.edu/labmembers/gordon/files/libgtextutils-0.6.tar.bz2 #note this is not latest version
tar -xjf libgtextutils-0.6.tar.bz2
cd libgtextutils-0.6
./configure
make
sudo make install

wget http://cancan.cshl.edu/labmembers/gordon/files/fastx_toolkit-0.0.12.tar.bz2 #note this is not latest version
tar -xjf fastx_toolkit-0.0.12.tar.bz2  
cd fastx_toolkit-0.0.12
./configure
make
g++ -DHAVE_CONFIG_H -I. -I../..   -I../libfastx   -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -DDEBUG -g -O1 -MT fastx_collapser.o -MD -MP -MF .deps/fastx_collapser.Tpo -c -o fastx_collapser.o fastx_collapser.cpp
fastx_collapser.cpp:50:10: fatal error: 'tr1/unordered_map' file not found
#include <tr1/unordered_map>
         ^
1 error generated.
make[3]: *** [fastx_collapser.o] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
cd src/
cd fastx_collapser
vi fastx_collapser.cpp
#press i to edit in vi

#original
#include <tr/unordered_map>
#new

#include <unordered_map>
#save and exit, press ESC and then type ":wq!"

cd ../..
make
fastx_collapser.cpp:51:6: error: no member named 'tr1' in namespace 'std'
std::tr1::unordered_map<string,size_t> collapsed_sequences;
~~~~~^
1 error generated.
make[3]: *** [fastx_collapser.o] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
cd src/fastx_collapser
vi fastx_collapser.cpp
#original

std::tr1::unordered_map<string,size_t> collapsed_sequences;
#new

std::unordered_map<string,size_t> collapsed_sequences;
sudo make install

Problem troubleshooted while installing Phylobayes on Mavericks by LM Davalos:

Problem: Parallel phylobayes (pb_mpi1.5a) does not compile from source on multi-processor mac running OS 10.9. After clearing out any errors having to do with open-mpi, these errors persist:

file BP2util.h

shell: fatal error: 'tr1/unordered_map' file not found

#include <tr1/unordered_map>

original #include <tr1/unordered_map> #tr1 is deprecated in 10.9 and will not compile

modified: #include <unordered_map>

shell: error: use of undeclared identifier 'tr1'

original: class BipartitionHashTable : public tr1::unordered_map<string,T> {};

modified: class BipartitionHashTable : public unordered_map<string,T> {};

file BP2Stat.h

shell: fatal error: 'tr1/unordered_map' file not found

#include <tr1/unordered_map>

original: #include <tr1/unordered_map>

modified: #include <unordered_map>

#define hash_map std::unordered_map

file PolyNode.cpp

shell: error: variable length array of non-POD element type 'string'

original:  string retval[degree]; #line 431

modified:  string *retval = new string[degree]; #line 431

brew install https://raw.github.com/Homebrew/homebrew-science/master/fastx_toolkit.rb

brew link --overwrite fastx_toolkit

Linking /usr/local/Cellar/fastx_toolkit/0.0.14... 

Error: Could not symlink include/gtextutils/gtextutils/container_join.h

/usr/local/include/gtextutils/gtextutils is not writable.

brew install https://raw.github.com/Homebrew/homebrew-science/master/fastx_toolkit.rb

######################################################################## 100.0%

Warning: fastx_toolkit-0.0.14 already installed, it's just not linked

sudo chown -R laurelyohe /usr/local/include

brew link --overwrite fastx_toolkit

Alright! I think it is installed. I have avoided using fastx-toolkit because it is such a pain in the butt to install, but alas, the uncertain has become certain. Why am I doing this? Because I am getting these alarming warning messages while Trinity is running. It seems to carry on regardless but it doesn't seem right.

...

warning: ignoring read XXXX since it cannot decipher if /1 or /2 of a pair.

Error: note that there were 4329123 reads that could not be deciphered as being /1 or /2 of a PE fragment. Hopefully, these were SE reads that should have been ignored. Otherwise, please research this further.

Okay, awesome. Seems like someone else ran into this problem:

http://sourceforge.net/p/trinityrnaseq/mailman/message/31448854/

After looking at what my input files were before and after trimming, it is clear that the fastq files have lost track of being from the right or left pair. Uggh! I knew that girl's Trinity help was too good to be true.

head Arjam_MOE_R1.fq

@HWI-ST885:197:HA2RPADXX:1:1101:1464:2292 1:N:0:ACAGTG

GCCCTTGCCGCCAGCTGGCGCGGCCACGCAGCGGCTGAGCGAGTCTAGGCGCGCGCTGTACTCGGTGAACTTCTTTTGGTAGCGCAGAGCAGTCATTTGC

+

CCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJIHHFDDCDDDDDDDDDDDCBBDBBBDDDDDEDDD@DDDDDDDDDDDDDACCDDDDDDDDDDDDDDEEED

@HWI-ST885:197:HA2RPADXX:1:1101:1438:2386 1:N:0:ACAGTG

GGGTGGAGCAAATTCTGGGCCAAAAGTAGTAGGTTCTGAAGGAGGAGGCAATGGTGGTGGTGGTGGACGTGGTCTCCTGAAGTGTCTGCGACTCTCACCA

+

CCCFFFFFDHHHHJGGHGIGIJJJHIFHIGIIJJJIIIIGHGGHI?FGHIGIIJ8@=5BEHHH9BEFEDCDDBDDDDDDCCD>@CCDDDDBDBBDDCCBC

@HWI-ST885:197:HA2RPADXX:1:1101:1310:2396 1:N:0:ACAGTG

CTTGGGTCGTGAGTGAGAACAGGCTGGTAGACGGGGCGCTCGCCGAAGGCTGGGATGAAGTCCCGAAACTAAACCCACCAGCGCTGGATGAGGAGAAAGA

head Arjam_MOE_R2.fq

@HWI-ST885:197:HA2RPADXX:1:1101:1464:2292 2:N:0:ACAGTG

CAACGGCGCGCTGCAGGCCCGGCTCGCCGCGCTGCACAAGGCTTTCAAGAAGGAGGCTCTGCGCGCAGGCAAGCGCGAGAAGTCGCTGGTGGCGCAGCTG

+

CCCFFFFFHHHHHJJJJJJIIJIEIBEHBBBBBDDD<CDDDDDDDCCDDDDDD?ABBBDDDDDDDBBDD@DDDDDDD<BBDDDDDDDBB<CBABD@BDDC

@HWI-ST885:197:HA2RPADXX:1:1101:1438:2386 2:N:0:ACAGTG

CCTGTTTCTCGCCTGGTGAGAGTCGCAGACACTTCAGGAGACCACGTCCACCACCACCACCATTGCCTCCTCCTTCAGAACCTACTACTTTTGGCCCAGA

+

BBBFFFFFHHGHHIJJGHHHHIGHIIIIJJJJJJJJJJIJIJFJJGHIIHJGHJJEHHHFFFFEEEEEEDDDDDDDDDDDDDDDDDDDDDEDDDDDDBDD

@HWI-ST885:197:HA2RPADXX:1:1101:1310:2396 2:N:0:ACAGTG

CAGGCGGGTTCACGTTTGGCACCGCAAAGACGGCGACAACCACCCCTGCCACCGGCTTTTCTTTCTCCTCATCCAGCGCTGGTGGGTTTAGTTTCGGGAC

Okay see how there is a 1 and a 2 in the title line?

head Arjam_MOE_R1_trim.fq

@HWI-ST885:197:HA2RPADXX:1:1101:1464:2292

GCCCTTGCCGCCAGCTGGCGCGGCCACGCAGCGGCTGAGCGAGTCTAGGCGCGCGCTGTACTCGGTGAACTTCTTTTGGTAGCGCAGAGCAGTCATTTGC

+

CCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJIHHFDDCDDDDDDDDDDDCBBDBBBDDDDDEDDD@DDDDDDDDDDDDDACCDDDDDDDDDDDDDDEEED

@HWI-ST885:197:HA2RPADXX:1:1101:1438:2386

GGGTGGAGCAAATTCTGGGCCAAAAGTAGTAGGTTCTGAAGGAGGAGGCAATGGTGGTGGTGGTGGACGTGGTCTCCTGAAGTGTCTGCGACTCTCACCA

+

CCCFFFFFDHHHHJGGHGIGIJJJHIFHIGIIJJJIIIIGHGGHI?FGHIGIIJ8@=5BEHHH9BEFEDCDDBDDDDDDCCD>@CCDDDDBDBBDDCCBC

@HWI-ST885:197:HA2RPADXX:1:1101:1310:2396

CTTGGGTCGTGAGTGAGAACAGGCTGGTAGACGGGGCGCTCGCCGAAGGCTGGGATGAAGTCCCGAAACTAAACCCACCAGCGCTGGATGAGGAGAAAGA

head Arjam_MOE_R2_trim.fq

@HWI-ST885:197:HA2RPADXX:1:1101:1464:2292

CAACGGCGCGCTGCAGGCCCGGCTCGCCGCGCTGCACAAGGCTTTCAAGAAGGAGGCTCTGCGCGCAGGCAAGCGCGAGAAGTCGCTGGTGGCGCAGCTG

+

CCCFFFFFHHHHHJJJJJJIIJIEIBEHBBBBBDDD<CDDDDDDDCCDDDDDD?ABBBDDDDDDDBBDD@DDDDDDD<BBDDDDDDDBB<CBABD@BDDC

@HWI-ST885:197:HA2RPADXX:1:1101:1438:2386

CCTGTTTCTCGCCTGGTGAGAGTCGCAGACACTTCAGGAGACCACGTCCACCACCACCACCATTGCCTCCTCCTTCAGAACCTACTACTTTTGGCCCAGA

+

BBBFFFFFHHGHHIJJGHHHHIGHIIIIJJJJJJJJJJIJIJFJJGHIIHJGHJJEHHHFFFFEEEEEEDDDDDDDDDDDDDDDDDDDDDEDDDDDDBDD

@HWI-ST885:197:HA2RPADXX:1:1101:1310:2396

CAGGCGGGTTCACGTTTGGCACCGCAAAGACGGCGACAACCACCCCTGCCACCGGCTTTTCTTTCTCCTCATCCAGCGCTGGTGGGTTTAGTTTCGGGAC

See how it goes away? Bollocks! This happens after running python ~/Scripts/q-trim.py.

Let's see if this strips it.

fastq_quality_filter -i Arjam_MOE_R1.fq -o Arjam_MOE_R1_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20

Minimum percentage: 80

Input: 15149790 reads.

Output: 14691119 reads.

head Arjam_MOE_R1_fastxtrimmed.fastq 

@HWI-ST885:197:HA2RPADXX:1:1101:1464:2292 1:N:0:ACAGTG

GCCCTTGCCGCCAGCTGGCGCGGCCACGCAGCGGCTGAGCGAGTCTAGGCGCGCGCTGTACTCGGTGAACTTCTTTTGGTAGCGCAGAGCAGTCATTTGC

+

CCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJIHHFDDCDDDDDDDDDDDCBBDBBBDDDDDEDDD@DDDDDDDDDDDDDACCDDDDDDDDDDDDDDEEED

@HWI-ST885:197:HA2RPADXX:1:1101:1438:2386 1:N:0:ACAGTG

GGGTGGAGCAAATTCTGGGCCAAAAGTAGTAGGTTCTGAAGGAGGAGGCAATGGTGGTGGTGGTGGACGTGGTCTCCTGAAGTGTCTGCGACTCTCACCA

+

CCCFFFFFDHHHHJGGHGIGIJJJHIFHIGIIJJJIIIIGHGGHI?FGHIGIIJ8@=5BEHHH9BEFEDCDDBDDDDDDCCD>@CCDDDDBDBBDDCCBC

@HWI-ST885:197:HA2RPADXX:1:1101:1310:2396 1:N:0:ACAGTG

CTTGGGTCGTGAGTGAGAACAGGCTGGTAGACGGGGCGCTCGCCGAAGGCTGGGATGAAGTCCCGAAACTAAACCCACCAGCGCTGGATGAGGAGAAAGA

Cool! Looks like it kept the extended header on.

fastq_quality_filter -i Arjam_MOE_R2.fq -o Arjam_MOE_R2_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20

Minimum percentage: 80

Input: 15149790 reads.

Output: 14464395 reads.

discarded 685395 (4%) low-quality reads.

For once something worked. Oh yeah, just as a side note if you have illumina reads you must put -Q 33 parameter. This of course, is an undocumented fix discovered by users. Three+ years after this discovery, -Q remains to be documented in the fastx-toolkit. 

I still am going to do the pair matching before running trinity again.

~/Scripts/both.py Arjam_MOE_R1_fastxtrimmed.fastq Arjam_MOE_R2_fastxtrimmed.fastq 

Trinity.pl --seqType fq --left Arjam_MOE_R1_fastxtrimmed.fastq.both --right Arjam_MOE_R2_fastxtrimmed.fastq.both --CPU 4 --JM 20G --output output_4

----------------------------------------------------------------

Yay! I fixed the /1 /2 problem. You can see that the fasta files trinity creates there is now the /1 and /2. Now we will see if we can get past chrysalis and if the other error with the c++libs is fixed.

head left.fa
>HWI-ST885:197:HA2RPADXX:1:1101:1464:2292/1
GCCCTTGCCGCCAGCTGGCGCGGCCACGCAGCGGCTGAGCGAGTCTAGGCGCGCGCTGTACTCGGTGAACTTCTTTTGGTAGCGCAGAGCAGTCATTTGC
>HWI-ST885:197:HA2RPADXX:1:1101:1438:2386/1
GGGTGGAGCAAATTCTGGGCCAAAAGTAGTAGGTTCTGAAGGAGGAGGCAATGGTGGTGGTGGTGGACGTGGTCTCCTGAAGTGTCTGCGACTCTCACCA
>HWI-ST885:197:HA2RPADXX:1:1101:1310:2396/1
CTTGGGTCGTGAGTGAGAACAGGCTGGTAGACGGGGCGCTCGCCGAAGGCTGGGATGAAGTCCCGAAACTAAACCCACCAGCGCTGGATGAGGAGAAAGA
>HWI-ST885:197:HA2RPADXX:1:1101:1346:2468/1
ATGGAGCCCAGGCCTCCAGTGCAGAGTGAGTGCTTCCTTCCATGGTCCCCATGCCATCGTGTGACAAGTTCTGTGACCTGATTTCCAGCACTGTCATCCA
>HWI-ST885:197:HA2RPADXX:1:1101:1467:2481/1
GGCCCAGGGAGTCCTCCACCACCCCCTCCCCTTTCCTGGCCTGCTCTCTAATTCTCTAGAAACCTTCCTGTGTATCCTGCCTACTTAAACCCTGCATCCC
head right.fa
>HWI-ST885:197:HA2RPADXX:1:1101:1464:2292/2
CAACGGCGCGCTGCAGGCCCGGCTCGCCGCGCTGCACAAGGCTTTCAAGAAGGAGGCTCTGCGCGCAGGCAAGCGCGAGAAGTCGCTGGTGGCGCAGCTG
>HWI-ST885:197:HA2RPADXX:1:1101:1438:2386/2
CCTGTTTCTCGCCTGGTGAGAGTCGCAGACACTTCAGGAGACCACGTCCACCACCACCACCATTGCCTCCTCCTTCAGAACCTACTACTTTTGGCCCAGA
>HWI-ST885:197:HA2RPADXX:1:1101:1310:2396/2
CAGGCGGGTTCACGTTTGGCACCGCAAAGACGGCGACAACCACCCCTGCCACCGGCTTTTCTTTCTCCTCATCCAGCGCTGGTGGGTTTAGTTTCGGGAC
>HWI-ST885:197:HA2RPADXX:1:1101:1346:2468/2
GGGGGTGGAAATTTTGAGACAAATGTTGATTCTTGGTGAGTTGATGAGTCTTTTCTAGACACATAGAGAAGGTGCTGAAGATTGAGAGAAAACGCCTTCC
>HWI-ST885:197:HA2RPADXX:1:1101:1467:2481/2

GTCAAACTCGTTGTAGCAGATTCTACTTGGGATGCAGGGTTTAAGTAGGCAGGATACACAGGAAGGTTTCTAGAGAATTAGAGAGCAGGCCAGGAAAGGG

To be continued.

Okay checked all my data and things were looking fishy and realized there were still some typos (missing a decimal point, etc.). Everything was carefully reexamined and I think (fingers crossed) these are official PCA results.

Had a minor panic attack because I realized my missing tarsus values were being imputed with mean of the bill length which of course would lead to extreme variance in the trait. Anyways, fixed it right up and still got somewhat similar results. Whew.
New PCA result:

Fixed script:
#impute missing values by taking mean of all other values of of other species ofthat character 

i<-1 #set the index
species.removed<-c()
#sift through all babbler species
while (i <= length(babblers$UniqueID_1)){
  #missing wing lengths; if the Wing Length is NA for that value
  if(is.na(babblers$Wing.Length[i]) == TRUE){
    #select the wing lengths of all birds which match this species with missing wing length
    wing.species.vector<-babblers$Wing.Length[which(babblers$Species[i] == babblers$Species)]
    #make a new vector without the missing value
    wing.species.filler<-wing.species.vector[which(is.na(wing.species.vector) == FALSE)]
    #calculate the mean
    wing.impute<-mean(wing.species.filler)
    #fill in missing value with the mean for that bird
    babblers$Wing.Length[i]<-wing.impute
  }
  
  #repeat the above method for all characters
  if(is.na(babblers$Tail.Length[i]) == TRUE){
    tail.species.vector<-babblers$Tail.Length[which(babblers$Species[i] == babblers$Species)]
    tail.species.filler<-tail.species.vector[which(is.na(tail.species.vector) == FALSE)]
    tail.impute<-mean(tail.species.filler)
    babblers$Tail.Length[i]<-tail.impute
  }
  
  
  
  if(is.na(babblers$Bill.Length[i]) == TRUE){
    BL.species.vector<-babblers$Bill.Length[which(babblers$Species[i] == babblers$Species)]
    BL.species.filler<-BL.species.vector[which(is.na(BL.species.vector) == FALSE)]
    BL.impute<-mean(BL.species.filler)
    babblers$Bill.Length[i]<-BL.impute
  }
  
  if(is.na(babblers$Bill.Width[i]) == TRUE){
    BW.species.vector<-babblers$Bill.Width[which(babblers$Species[i] == babblers$Species)]
    BW.species.filler<-BW.species.vector[which(is.na(BW.species.vector) == FALSE)]
    BW.impute<-mean(BW.species.filler)
    babblers$Bill.Width[i]<-BW.impute
  }
  
  if(is.na(babblers$Bill.Depth[i]) == TRUE){
    BD.species.vector<-babblers$Bill.Depth[which(babblers$Species[i] == babblers$Species)]
    BD.species.filler<-BD.species.vector[which(is.na(BD.species.vector) == FALSE)]
    BD.impute<-mean(BD.species.filler)
    babblers$Bill.Depth[i]<-BD.impute
  }
  
  if(is.na(babblers$Tarsus.Length[i]) == TRUE){
    TL.species.vector<-babblers$Tarsus.Length[which(babblers$Species[i] == babblers$Species)]
    TL.species.filler<-TL.species.vector[which(is.na(TL.species.vector) == FALSE)]
    TL.impute<-mean(TL.species.filler)
    babblers$Tarsus.Length[i]<-TL.impute
  }
  
  if(is.na(babblers$Hallux[i]) == TRUE){
    hallux.species.vector<-babblers$Hallux[which(babblers$Species[i] == babblers$Species)]
    hallux.species.filler<-hallux.species.vector[which(is.na(hallux.species.vector) == FALSE)]
    hallux.impute<-mean(hallux.species.filler)
    babblers$Hallux[i]<-hallux.impute
  }

  i<-i+1
}

When running PRGmatic v1.7, if you get an error:

"Can't exec "./cap3": No such file or directory at ./PRGmatic.pl line 116, <STDIN> line 8.
contigFile is Species_01_trimmed.fasta.cap.contigs
No such file or directory at ./PRGmatic.pl line 127, <STDIN> line 8."

Go to PRGmatic folder in home directory (or wherever it is), click >Dependent Software and you probably need to unzip "cap3.macosx.intel64.zip". Unzip this this folder and move all of the contents to the PRGmatic main directory.