run_CSTACKS_by_hand2.sh

#!/bin/bash
#PBS -M [your email]
#PBS -m abe
#PBS -l nodes=1:ppn=16
#PBS -l walltime=350:00:00
#PBS -N CSTACKS
#PBS -q default
#PBS -j oe
#PBS -o /PATH/TO/Stacks/JOBS/OUT/cstacks_T90.out

OUTDIR="/PATH/TO/Stacks/RESULTS6_T90" # same as USTACKS
pPARAM=$PBS_NP
nPARAM=1
k_lenPARAM=10

#Removi 2 amostras MG20_16; MG20_17

CSTACKS_CMMD="
A_RS1
A_RS10
A_RS11
A_RS12
A_RS13
A_RS14
A_RS15
A_RS16
A_RS17
A_RS18
A_RS19
A_RS2
A_RS20
A_RS21
A_RS24
A_RS25
A_RS26
A_RS27
A_RS28
A_RS29
A_RS3
A_RS31
A_RS32
A_RS33
A_RS4
A_RS5
A_RS6
A_RS7
A_RS8
A_RS9
BA34_1
BA34_10
BA34_11
BA34_12
BA34_13
BA34_14
BA34_15
BA34_16
BA34_17
BA34_18
BA34_19
BA34_2
BA34_20
BA34_21
BA34_22
BA34_23
BA34_24
BA34_25
BA34_26
BA34_27
BA34_28
BA34_29
BA34_3
BA34_30
BA34_4
BA34_5
BA34_6
BA34_7
BA34_8
BA34_9
GO30_1
GO30_10
GO30_11
GO30_12
GO30_13
GO30_14
GO30_15
GO30_16
GO30_17
GO30_18
GO30_19
GO30_2
GO30_20
GO30_21
GO30_22
GO30_23
GO30_24
GO30_25
GO30_26
GO30_27
GO30_28
GO30_29
GO30_3
GO30_30
GO30_4
GO30_5
GO30_6
GO30_7
GO30_7
GO30_7
GO30_7
GO30_8
GO30_9
GO31_1
GO31_10
GO31_11
GO31_12
GO31_13
GO31_14
GO31_15
GO31_16
GO31_17
GO31_18
GO31_19
GO31_2
GO31_20
GO31_21
GO31_22
GO31_23
GO31_24
GO31_25
GO31_26
GO31_27
GO31_28
GO31_29
GO31_3
GO31_30
GO31_4
GO31_5
GO31_6
GO31_7
GO31_8
GO31_9
MG20_1
MG20_10
MG20_11
MG20_12
MG20_13
MG20_14
MG20_15
MG20_18
MG20_19
MG20_2
MG20_20
MG20_21
MG20_22
MG20_23
MG20_24
MG20_25
MG20_26
MG20_27
MG20_28
MG20_29
MG20_3
MG20_30
MG20_4
MG20_5
MG20_6
MG20_7
MG20_8
MG20_9
PR51_1
PR51_10
PR51_11
PR51_12
PR51_13
PR51_14
PR51_15
PR51_16
PR51_17
PR51_18
PR51_19
PR51_2
PR51_20
PR51_21
PR51_22
PR51_23
PR51_24
PR51_25
PR51_26
PR51_27
PR51_28
PR51_29
PR51_3
PR51_30
PR51_4
PR51_5
PR51_6
PR51_7
PR51_8
PR51_9
PR52_1
PR52_10
PR52_11
PR52_12
PR52_13
PR52_14
PR52_15
PR52_16
PR52_17
PR52_18
PR52_19
PR52_2
PR52_20
PR52_21
PR52_22
PR52_23
PR52_24
PR52_25
PR52_26
PR52_27
PR52_28
PR52_29
PR52_3
PR52_4
PR52_5
PR52_6
PR52_7
PR52_8
PR52_9
RS16_1
RS16_10
RS16_11
RS16_12
RS16_13
RS16_14
RS16_15
RS16_16
RS16_17
RS16_18
RS16_19
RS16_2
RS16_20
RS16_21
RS16_22
RS16_23
RS16_24
RS16_25
RS16_26
RS16_27
RS16_28
RS16_29
RS16_3
RS16_30
RS16_4
RS16_5
RS16_6
RS16_7
RS16_8
RS16_9
RS17_1
RS17_10
RS17_11
RS17_12
RS17_13
RS17_14
RS17_15
RS17_16
RS17_17
RS17_18
RS17_19
RS17_2
RS17_20
RS17_21
RS17_22
RS17_23
RS17_24
RS17_25
RS17_26
RS17_27
RS17_28
RS17_29
RS17_3
RS17_30
RS17_4
RS17_5
RS17_6
RS17_7
RS17_8
RS17_9
SC3_1
SC3_10
SC3_11
SC3_12
SC3_13
SC3_14
SC3_15
SC3_16
SC3_17
SC3_18
SC3_19
SC3_2
SC3_20
SC3_21
SC3_22
SC3_23
SC3_24
SC3_25
SC3_26
SC3_27
SC3_28
SC3_29
SC3_3
SC3_30
SC3_4
SC3_5
SC3_6
SC3_7
SC3_8
SC3_9
SP17_1
SP17_10
SP17_11
SP17_12
SP17_13
SP17_14
SP17_15
SP17_16
SP17_17
SP17_18
SP17_19
SP17_2
SP17_20
SP17_21
SP17_22
SP17_23
SP17_24
SP17_25
SP17_26
SP17_27
SP17_28
SP17_29
SP17_3
SP17_30
SP17_4
SP17_5
SP17_6
SP17_6
SP17_6
SP17_7
SP17_8
SP17_9"

# 
# Use a loop to create a list of files to supply to cstacks.
#
samp=""
for file in $CSTACKS_CMMD
do 
    samp+="-s $OUTDIR/$file ";
done

# 
# Build the catalog; the "&>>" will capture all output and append it to the Log file.
#
# Need to export due to GCC 6.1.0
export PATH LD_LIBRARY_PATH
PATH=/share/programs/gcc/6.1.0/bin/:$PATH
echo $LD_LIBRARY_PATH
LD_LIBRARY_PATH=/share/programs/gcc/6.1.0/lib/:/share/programs/gcc/6.1.0/lib64/:$LD_LIBRARY_PATH 

~/programs/stacks/stacks-1.40/cstacks -p $pPARAM -b 5 -n $nPARAM -o $OUTDIR --k_len $k_lenPARAM $samp