E&S

This page could have been a Q&A (Questions & Answers), but instead I have decided to call it an E&S - Error messages and Solutions!

zorro

Error message:


mats@Slartibartfasts:~/project/tic22/master$ zorro Tic22_outgroup.4.linsi.fst > out.txt

error: Cannot create tree from alignment 
 Check FastTree installation
  exiting...

Solution: My installation works with the example file distributed with the program, so I suppose the problem is the fasta file I'm trying to analyse. A typical fasta header in the file looks something like ">Linum_usitatissimum gnl|BL_ORD_ID|39140 10009759|PACid 23178320".

  • Check that all fasta headers are unique.
  • Remove the characters ":,()" from the sequence names.
  • Remove spaces from the sequence names.

MrBayes v.3.2

Error message #1:

...

      Number of chains on processor 6 = 1
      Number of chains on processor 7 = 1
      Number of chains on processor 8 = 1
      Number of taxa = 105
      Number of characters = 2002
      Compressing data matrix for division 1
      Division 1 has 282 unique site patterns
      The MCMC sampler will use the following moves:
         With prob.  Chain will use move
           19.23 %   eSS(Tau,V)
           19.23 %   eTBR(Tau,V)
           38.46 %   pSPR(Tau,V)
           19.23 %   Multiplier(V)
            3.85 %   Uniform(Aamodel)

      Creating parsimony (bitset) matrix for division 1
      Initializing conditional likelihoods for terminals
      Initializing conditional likelihoods for internal nodes
      Allocating space for parsimony sets
      Initial log likelihoods and log prior probs for run 1:
         Chain 1 -- -56327.889100 -- -176.482300
      There are 7 more chains on other processor(s)

      Chain results:

         1 -- (-56273.020) [...7 remote chains...] 
[compute-0-0:13441] *** Process received signal ***
[compute-0-0:13441] Signal: Segmentation fault (11)
[compute-0-0:13441] Signal code:  (128)
[compute-0-0:13441] Failing at address: (nil)
[compute-0-0:13441] [ 0] /lib64/libpthread.so.0 [0x3fa1c0e7c0]
[compute-0-0:13441] [ 1] /lib64/libc.so.6(vsnprintf+0x84) [0x3fa1469874]
[compute-0-0:13441] [ 2] /usr/local/bin/mb-3.2(SafeSprintf+0xba) [0x43dc7a]
[compute-0-0:13441] [ 3] /usr/local/bin/mb-3.2(PrintTree+0x430) [0x443700]
[compute-0-0:13441] [ 4] /usr/local/bin/mb-3.2(PrintStatesToFiles+0x720) [0x47bf30]
[compute-0-0:13441] [ 5] /usr/local/bin/mb-3.2(RunChain+0x1382) [0x482622]
[compute-0-0:13441] [ 6] /usr/local/bin/mb-3.2(DoMcmc+0x731) [0x484661]
[compute-0-0:13441] [ 7] /usr/local/bin/mb-3.2(ParseCommand+0x285) [0x425d05]
[compute-0-0:13441] [ 8] /usr/local/bin/mb-3.2(DoExecute+0x620) [0x426bd0]
[compute-0-0:13441] [ 9] /usr/local/bin/mb-3.2(ParseCommand+0x285) [0x425d05]
[compute-0-0:13441] [10] /usr/local/bin/mb-3.2(CommandLine+0x161) [0x410621]
[compute-0-0:13441] [11] /usr/local/bin/mb-3.2(main+0x7c) [0x4108ec]
[compute-0-0:13441] [12] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3fa141d994]
[compute-0-0:13441] [13] /usr/local/bin/mb-3.2 [0x40e6b9]
[compute-0-0:13441] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 3 with PID 13441 on node compute-0-0.local exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------

Solution:

One of the sequence names is to long. In this case it is this one:

[97] Cyanophora_paradoxa_gnl_BL_ORD_ID_26154__Cyanophora_parensusfromContig52820-snap-gene-0.3-mRNA-1_cds_10085_8432-8552_0_-

A 100 character long sequence name is OK though.


Error message #2:

MrBayes > sumt

   Summarizing trees in files "Tic22_outgroup.6.linsi.nex.run1.t" and "Tic22_outgroup.6.linsi.nex.run2.t"
   UNIX line termination
   Examining first file ...
   Found one tree block in file "Tic22_outgroup.6.linsi.nex.run1.t" with 5431 trees in last block
   Expecting the same number of trees in the last tree block of all files

   Tree reading status:

   0      10      20      30      40      50      60      70      80      90     100
   v-------v-------v-------v-------v-------v-------v-------v-------v-------v-------v
   *   Expecting 
   Instead found '1.000000e-01' in command 'Tree'
   Error in command "Sumt"

MrBayes > 

Solution:

This happens when trying to run the sumt command in MrBayes v.3.1.2 on tree files generated using version 3.2.


Error message #3:

CUDA error: "Invalid device" from file , line 215.

Solution: This happens when I'm running more that one MrBayes analysis on the "gpu" queue on the University of Leicester cluster Alice. No solution for the problem yet.


MrBayes v.3.1.2

Error message:

[compute-0-4:03414] *** Process received signal ***
[compute-0-4:03414] Signal: Segmentation fault (11)
[compute-0-4:03414] Signal code: Address not mapped (1)
[compute-0-4:03414] Failing at address: 0x10
[compute-0-4:03414] [ 0] /lib64/libpthread.so.0 [0x39d2a0e7c0]
[compute-0-4:03414] [ 1] /opt/bio/mrbayes/mb(ConTree+0x6f2) [0x4c16c2]
[compute-0-4:03414] [ 2] /opt/bio/mrbayes/mb(DoSumt+0x3ec) [0x4c25cc]
[compute-0-4:03414] [ 3] /opt/bio/mrbayes/mb(ParseCommand+0x321) [0x41f7d1]
[compute-0-4:03414] [ 4] /opt/bio/mrbayes/mb(CommandLine+0x172) [0x40dc62]
[compute-0-4:03414] [ 5] /opt/bio/mrbayes/mb(main+0x18f) [0x40e13f]
[compute-0-4:03414] [ 6] /lib64/libc.so.6(__libc_start_main+0xf4) [0x39d221d994]
[compute-0-4:03414] [ 7] /opt/bio/mrbayes/mb [0x40bc49]
[compute-0-4:03414] *** End of error message ***
[compute-0-2.local][[1144,1],2][btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 3414 on node
compute-0-4.local exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------

Solution: This happens on a 64-bit system from time to time when running the sumpt command using MrBayes 3.1.2. I have not found a good explanation for this bug. Use a binary of MrByes that is compiled on a 32-bit system WITHOUT the readline library to solve this problem. You can use the command "mb-noreadline.32" if you have access to the Albiorix cluster.


fastqc

Error message:

Exception in thread "Thread-6" java.lang.NullPointerException
        at uk.ac.bbsrc.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:115)
        at uk.ac.bbsrc.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:79)
        at uk.ac.bbsrc.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:76)
        at java.lang.Thread.run(Thread.java:679)

Sometimes encounter this (or similar?) error messages when running "fastqc". No solution yes, but I suspect this may have to do with disk space problems.


ssh

Error message:

ssh_exchange_identification: Connection closed by remote host

or

ssh: connect to host albiorix.bioenv.gu.se port 22: Connection refused

Solution: The first message is often seen when the server you are attempting to connect to is being busy serving logon requests from a bot-server. On Albiorix, the second message means that your IP address could have been banned, due to to many failed password attempts. Contact your systems administrator.