hh-suite
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soedinglab
Odd "residue" written to consensus sequence depending on value of `-M`
Current Behavior
hhconsensus writes an odd "residue" character at the end of the consensus sequence depending on value of -M.
From -M50 (copying and pasting what is shown by less:
#DGTL1_BRASO L=1 39.856 8190 pos. 9 - 381 [ 1, -1] S|A4YV79|DGTL1_BRASO
>DGTL1_BRASO_consensus
MTTMMMTMRMDP-------------IGFEYAELAPYASDPAVSRGRLYPE--ERESDTRSPFQRDRDRIIHSAAFRRLQYKTQVFINHE-----GDHYRTRLTHSLEVAQIARSIARALG---------------------------LDEDLAEAIALAHDLGHPPFGHAGERALNECMKDYGG-----FEHNAQSLRIVTKLEPRYADF---------DGLNLTRETLEGIVKHPGPLTGPSGAPAGRKFGFY----VPDDIADYNWVKDLELDD------------------------------------FASLEAQVMDLADDIAYNVHDLEDGLRAGLITLEQLQEV--PLLAALADEVKRRYPDLDPDRLISEAVRLLINAIVEDVIAFITSTQARLALKRPTSEDDVRFLGYAIVAFSAAMR----------------------------------------------EELAVLKKFLFQNVYRHPRVQRIEYKARRIIQDLFEAYMADPELLPPPYWARIWEEAEDD-AARARVIADYIAGMTDRYALREYQRLFDPTPDLRFKFIYEYI<E9> ^C
>DGTL1_BRASO L=1 39.856 8190 pos. 9 - 381 [ 1, -1] S|A4YV79|DGTL1_BRASO
----------MS-------------VGMA-APRAPYSCDPDRSRGRLFAE---PPSRTRSPFRRDCDRVIHSTAFRRLKHKTQVFVFHE-----GDHYRTRLTHSLEVAQIARALARQLG---------------------------LDEDLTETLALAHDLGHPPFGHAGERALNRCMADHGG-----FDHNAQTLRIVTAFEQRYPDF---------DGLNLTWESLEGIVKHNGPLQG------------P----VPAGIAEFNARFDLELWS------------------------------------YASLEAQVAALADDIAYDAHDIDDGLRAGLFTVDDLKEV--PLLAAIIAEIDRHYPSLDDIRRGAELVRELISYLIAAVAG---EAERRIEQAKPVSPHDVRRHAGPLVAFPADVA----------------------------------------------EHEATIKAFLWQRMYRHERVMRVMRDAERIVADLFGRYQQDGATLPAGWL--DGCGG--E-GERARRISHFIAGMTDRFALTEHHRLFDSTPDLR--------
Expected Behavior
This should not happen...
Steps to Reproduce (for bugs)
See MF_01212.txt attached to this issue.
[saladi1@comet-ln2 hamap]$ hhconsensus -i MF_01212.txt -ofas test30.txt -M 30
- 10:55:41.187 INFO: MF_01212.txt is in A2M, A3M or FASTA format
[saladi1@comet-ln2 hamap]$ hhconsensus -i MF_01212.txt -ofas test40.txt -M 40
- 10:55:45.523 INFO: MF_01212.txt is in A2M, A3M or FASTA format
[saladi1@comet-ln2 hamap]$ hhconsensus -i MF_01212.txt -ofas test50.txt -M 50
- 10:55:49.430 INFO: MF_01212.txt is in A2M, A3M or FASTA format
[saladi1@comet-ln2 hamap]$ hhconsensus -i MF_01212.txt -ofas test60.txt -M 60
- 10:55:52.893 INFO: MF_01212.txt is in A2M, A3M or FASTA format
[saladi1@comet-ln2 hamap]$ hhconsensus -i MF_01212.txt -ofas test70.txt -M 70
- 10:55:55.993 INFO: MF_01212.txt is in A2M, A3M or FASTA format
HH-suite Output (for bugs)
MF_01212.txt test70.txt test60.txt test50.txt test40.txt test30.txt
Context
Providing context helps us come up with a solution and improve our documentation for the future.
Your Environment
- build
hh-suite commit: d335e62
HHconsensus 3.1.0
- Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 63
model name : Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
stepping : 2
microcode : 61
cpu MHz : 2501.000
cache size : 30720 KB
physical id : 0
siblings : 12
core id : 0
cpu cores : 12
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 15
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm ida arat epb xsaveopt pln pts dtherm invpcid_single ssbd pti retpoline ibrs ibpb tpr_shadow vnmi flexpriority ept vpid fsgsbase bmi1 avx2 smep bmi2 erms invpcid cqm cqm_llc cqm_occup_llc
bogomips : 4988.39
clflush size : 64
cache_alignment : 64
address sizes : 46 bits physical, 48 bits virtual
power management:
- Operating system and version:
[saladi1@comet-ln3 ~]$ cat /etc/centos-release
CentOS release 6.10 (Final)
[saladi1@comet-ln3 ~]$ cat /etc/lsb-release
LSB_VERSION=base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
[saladi1@comet-ln3 ~]$ uname -a
Linux comet-ln3.sdsc.edu 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
[saladi1@comet-ln3 ~]$ locale
LANG=en_US.UTF-8
LC_CTYPE=en_US.UTF-8
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=
hey @smsaladi, did you manage to find a solution for this? I am having the same problem.
