I am trying to use MetaClusterTA (http://i.cs.hku.hk/~alse/MetaCluster/download.html) for binning and annotating my metatranscriptomic dataset. To start with, I do it with a simulated dataset that I created with NeSSM and alignment performed by transabyss.

I followed the instructions in the MetaClusterTA README file, I downloaded the database and created the taxid file in the format as described.

However, when I try to run it fails. I tried several options, but none of them seems to be working.

Here is the output:

/software/MetaClusterTA/bin/MetaCluster_TA ~/simulated_dataset/simulation_1.fq ~/simulated_dataset/simulation_2.fq ~/transabyss-final.fa ~/taxids.csv --ReadLen 75 --Species 50 --MaxSpecies 1000

ReadLen:     75
CtgLenThresh:    500
AlignThresh:     76
MC3_Thresh: 0.94
before loading genomes.
0 out of 30269 genomes are loaded.
Finished counting occurences in strings. 
Finished mallocing vectors in nodes. 
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
alba      6834 98.4  3.1 17342688 16812812 pts/5 Sl+ 13:40   0:36 /software/MetaClusterTA/bin/MetaCluster
[...]

Finished mapping k-mers in strings. 
Finished sorting vectors in nodes. 
Finished turning capacity to number of unique id num. 
Genome DB Initialization is finished.
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
alba      6834  100  3.1 17342688 16812812 pts/5 Sl+ 13:40   0:37 /software/MetaClusterTA/bin/MetaCluster
[...]

initializing reads. 
Wed May 11 13:41:01 2016
initializing uset: 
Wed May 11 13:44:50 2016
NumNodes:   0
Size:   0
ReverSize:  512
sumlen: 0
MaxSpecies: 2
MinSpecies: 2
MaxSpecies is too large. We will start with half of the group number.
Size:0, classes:50
Segmentation fault (core dumped)

The aligned file looks like this:

>R184409 1327 23064 153518-,...,157386-
CCGGGCGACGGTTGTCCCGGTTTAAGCGTGCAGGTGGGTGGACCAGGCAAATCCGGTCTGCTGTAACACTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGTGACAGATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACACGAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGGCGCGTAGGTGAAGGGACTTGCTCCCGGAGCTGAAGCCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTATCCGCAAGGAGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGTACCCGCGGCAAGACGGAAAGACCCCGTGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGGCTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCAACCTTGAAATACCACCCTTTAATGTTTGATGTTCTAACGTGGACCCGTGATCCGGGTTGCGGACAGTGTCTGGTGGGTAGTTTGACTGGGGCGGTCTCCTCCCAAAGAGTAACGGAGGAGCACGAAGGTGGGCTAATCACGGTTGGACATCGTGAGGTTAGTGCAATGGCATAAGCCCGCTTGACTGCGAGAATGACAATTCGAGCAGGTGCGAAAGCAGGTCATAGTGATCCGGTGGTTCTGAATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGAATTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCATTGCCCGGTAGCTACGTTCGGAACTGATAACCGCTGAAAGCATCTAAGCGGGAAGCC
>R184410 2220 66038 169714+,...,118906+
GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGACAGCAGGCTCATAAGACGCCCCAGCGTCGCCATAGTGCGTTCACCGAATACGTGCGCAACAACCGTCTTCCGGAGACTGTCATACGCGTAAAACAGCCAGCGCTGGCGCGATTTAGCCCCGACATAGCCCCACTGTTCGTCCATTTCCGCGCAGACGATGACGTCACTGCCCGGCTGTATGCGCGAGGTTACCGACTGCGGCCTGAGTTTTTTAAGTGACGTAAAATCGTGTTGAGGCCAACGCCCATAATGCGTGCAGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCACAAAATAGTCATGCATTGTGTGCAATAGAAACAGTTCAGATAAAGATAGGGATTAGACTGGCCCCCTGAATCTCCAGACAACCAGTATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGTACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTTCTCTGGCGTAAGCAATACCAGGAAGGAAGTCTTACTGCTGTCGCCGCCGGAGAACAGGTTGTTCCTGCCTCTGAACTTGCTGCCGCCATGAAGCAGATTAAAGAACTCCAGCGCCTGCTCGGCAAGAAAACGATGGAAAATGAACTCCTCAAAGAAGCCGTTGAATATGGACGGGCAAAAAAGTGGATAGCGCACGCGCCCTTATTGCCCGGGGATGGGGAGTAAGCTTAGTCAGCCGTTGTCTCCGGGTGTCGCGTGCGCAGTTGCACGTCATTCTCAGACGAACCGATGACTGGATGGATGGCCGCCGCAGTCGTCACACTGATGATACGGATGTGCTTCTCCGTATACACCATGTTATCGGAGAGCTGCCCACGTATGGTTATCGTCGGGTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCTGTTGCTTGAGCGAAAACCTGCTGTACCGCCATCGAAACGGGCACATACAGGCAGAGTGGCCGTGAAAGAAAGCAATCAGCGATGGTGCTCTGACGGGTTCGAGTTCTGCTGTGATAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTGACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACGGGGATACCAGTTCAACCGAAAACGCCAGAGGAGGGGATTACCCGCTGGCAGGGTAAATCTGTGG
[...]

The taxid.csv file looks like this:

superkingdom_id phylum_id       class_id        order_id        family_id       genus_id        species_id      path_to_genome
2       544448  31969   2085    2092    2129    134821  /home/alba/test/Ureaplasma_parvum_serovar_3_ATCC_700970_uid57711/NC_002162.fna
2157    28890   183963  2235    2236    2239    2242    /home/alba/test/Halobacterium_NRC_1_uid57769/NC_002607.fna
2       1224    1236    91347   543     590     28901   /home/alba/test/Salmonella_enterica_serovar_Typhimurium_LT2_uid57799/NC_003197.fna
2       1224    1236    118969  118968  776     777     /home/alba/test/Coxiella_burnetii_RSA_493_uid57631/NC_002971.fna
2157    28890   183939  2182    2183    2184    39152   /home/alba/test/Methanococcus_maripaludis_S2_uid58035/NC_005791.fna
2       1239    186801  186802  543349  2733    2734    /home/alba/test/Symbiobacterium_thermophilum_IAM_14863_uid58165/NC_006177.fna
2       1224    1236    135623  641     511678  668     /home/alba/test/Vibrio_fischeri_ES114_uid58163/NC_006840.fna