diff --git a/src/gsi/correlated_obsmod.F90 b/src/gsi/correlated_obsmod.F90
index bda2c1eea..94834bde1 100644
--- a/src/gsi/correlated_obsmod.F90
+++ b/src/gsi/correlated_obsmod.F90
@@ -410,8 +410,8 @@ subroutine set_(instrument,fname,mask,method,kreq,kmut,ErrorCov)
            if (iuse_rad(ii)>0) then
               coun=coun+1
            endif
+           nctotf=nctotf+1
         endif
-        nctotf=nctotf+1
       enddo
 !     if no data available, turn off Correlated Error
       if (coun==0) then
@@ -462,7 +462,6 @@ subroutine set_(instrument,fname,mask,method,kreq,kmut,ErrorCov)
         do ii=1,ErrorCov%nch_active
            indR=0
            do jj=couns,nch_active 
-!              if (indxR(jj)==ErrorCov%indxR(ii)) then
               if (indxR(jj)==indxRf(ii)) then
                  indR=jj
                  couns=jj+1
@@ -484,7 +483,6 @@ subroutine set_(instrument,fname,mask,method,kreq,kmut,ErrorCov)
          do ii=1,nch_active
            indR=0
            do jj=couns,ErrorCov%nch_active
-!           if (ErrorCov%indxR(jj)==indxR(ii)) then
               if (indxRf(jj)==indxR(ii)) then
                  indR=jj
                  couns=jj+1
diff --git a/util/Correlated_Obs/cov_calc.f90 b/util/Correlated_Obs/cov_calc.f90
index bb377edba..3482f0fcf 100644
--- a/util/Correlated_Obs/cov_calc.f90
+++ b/util/Correlated_Obs/cov_calc.f90
@@ -332,18 +332,12 @@ program cov_calc
    deallocate(Rcovbig,divbig,ges_avebig1,ges_avebig2)
    deallocate(n_pair_hl, obs_pairs_hl)
 end if
-reclen=kind(Rcov(1,1))
-open(22,file='Rcov_iasicland',form='unformatted')
-read(22) nch_active, nctot, reclen
-read(22) indR
-read(22) Rcov
-close(22)
 !output
 reclen=kind(Rcov(1,1))
 open(26,file=trim(cov_file),form='unformatted')
 write(26) nch_active, nctot, reclen
-write(26) indRf
-write(26) Rcov
+write(26) indRf(1:nch_active)
+write(26) Rcov(1:nch_active,1:nch_active)
 close(26)
 
 if (out_wave) then
@@ -361,8 +355,6 @@ program cov_calc
    write(25,rec=1) Rcorr
    close(25)
 end if
-!KAB
-print *, indRf
 deallocate(Rcov,chaninfo,errout)
 deallocate(indR,indRf)
 deallocate(divider)
diff --git a/util/Correlated_Obs/readsatobs.f90 b/util/Correlated_Obs/readsatobs.f90
index a6316684a..2bf67942e 100644
--- a/util/Correlated_Obs/readsatobs.f90
+++ b/util/Correlated_Obs/readsatobs.f90
@@ -113,7 +113,7 @@ subroutine get_chaninfo_nc(filename,chan_choice)
    character(len=9), intent(in)  :: filename
    integer(i_kind), intent(in):: chan_choice
    integer(i_kind) iunit, nobs, i,j
-   integer(i_kind), dimension(:), allocatable ::Use_Flag,chind,shind
+   integer(i_kind), dimension(:), allocatable ::Use_Flag,chind,schind
    real(r_double), dimension(:), allocatable:: Waves,Inv_Errors
    real(r_kind), dimension(:), allocatable:: Wave,Inv_Error
 
@@ -122,13 +122,13 @@ subroutine get_chaninfo_nc(filename,chan_choice)
    nobs = nc_diag_read_get_dim(iunit,'nobs')
    if (nobs <= 0) call nc_diag_read_close(filename)
    nctot = nc_diag_read_get_dim(iunit,'nchans')
-   allocate(Use_Flag(nctot),chind(nobs),shind(nctot),Wave(nctot),Inv_Error(nctot))
+   allocate(Use_Flag(nctot),chind(nobs),schind(nctot),Wave(nctot),Inv_Error(nctot))
    allocate(Waves(nctot),Inv_Errors(nctot))
    call nc_diag_read_get_var(iunit, 'use_flag', Use_Flag)
    call nc_diag_read_get_var(iunit, 'Channel_Index', chind)
    call nc_diag_read_get_var(iunit, 'wavenumber', Waves)
    call nc_diag_read_get_var(iunit, 'error_variance', Inv_Errors)
-   call nc_diag_read_get_var(iunit, 'sensor_chan', shind)
+   call nc_diag_read_get_var(iunit, 'sensor_chan', schind)
    Wave=real(Waves,r_kind)
    Inv_Error=real(Inv_Errors,r_kind)
    call nc_diag_read_close(filename)
@@ -144,13 +144,12 @@ subroutine get_chaninfo_nc(filename,chan_choice)
    allocate(indRf(nch_active),indR(nch_active),chaninfo(nch_active),errout(nch_active))
    i=0
    do j=1,nctot
-print *, 'chan ', shind(j)
       if (chan_choice==full_chan) then
-         indRf(j)=shind(j)!j
+         indRf(j)=schind(j)
          indR(j)=j
       else if (Use_Flag(chind(j))>0) then
          i=i+1
-         indRf(i)=shind(j)!j
+         indRf(i)=schind(j)
          indR(i)=j
       end if
    end do
@@ -158,7 +157,7 @@ subroutine get_chaninfo_nc(filename,chan_choice)
       chaninfo(j)=Wave(chind(indR(j)))
       errout(j)=Inv_Error(chind(indR(j)))
    end do
-   deallocate(Use_flag,chind,Wave,Inv_Error,Waves,Inv_Errors)
+   deallocate(Use_flag,chind,schind,Wave,Inv_Error,Waves,Inv_Errors)
 end subroutine get_chaninfo_nc
 
 ! read radiance data