Closed olli0601 closed 8 years ago
Hi Chris, Running phylotype.py as below, I get the following error:
1 60 1 60 Traceback (most recent call last): File "/work/or105/libs/phylotypes/phylotypes.py", line 634, in FirstSeq = str(AllSeqsToPrint[0].seq) IndexError: list index out of range
Do you have an idea what s going on? Thanks! olli
module load intel-suite/2015.1 mpi R/3.2.0 raxml/8.2.4 mafft/7 anaconda/2.3.0 samtools CWD=$(pwd) echo $CWD mkdir -p "$CWD/pty_16-01-20-13-35-09" cp "/work/or105/Gates_2014/2015_PANGEA_DualPairsFromFastQIVA/ptyruns/ptyr2_bam.txt" "$CWD/pty_16-01-20-13-35-09" cp "/work/or105/Gates_2014/2015_PANGEA_DualPairsFromFastQIVA/ptyruns/ptyr2_ref.txt" "$CWD/pty_16-01-20-13-35-09" cd "$CWD/pty_16-01-20-13-35-09" /work/or105/libs/phylotypes/phylotypes.py 3 2 "ptyr2_bam.txt" "ptyr2_ref.txt" 1 60 61 120 121 180 181 240 241 300 301 360 361 420 421 480 481 540 541 600 601 660 661 720 721 780 781 840 841 900 901 960 961 1020 1021 1080 1081 1140 1141 1200 1201 1260 1261 1320 1321 1380 1381 1440 1441 1500 1501 1560 1561 1620 1621 1680 1681 1740 1741 1800 1801 1860 1861 1920 1921 1980 1981 2040 2041 2100 2101 2160 2161 2220 2221 2280 2281 2340 2341 2400 2401 2460 2461 2520 2521 2580 2581 2640 2641 2700 2701 2760 2761 2820 2821 2880 2881 2940 2941 3000 3001 3060 3061 3120 3121 3180 3181 3240 3241 3300 3301 3360 3361 3420 3421 3480 3481 3540 3541 3600 3601 3660 3661 3720 3721 3780 3781 3840 3841 3900 3901 3960 3961 4020 4021 4080 4081 4140 4141 4200 4201 4260 4261 4320 4321 4380 4381 4440 4441 4500 4501 4560 4561 4620 4621 4680 4681 4740 4741 4800 4801 4860 4861 4920 4921 4980 4981 5040 5041 5100 5101 5160 5161 5220 5221 5280 5281 5340 5341 5400 5401 5460 5461 5520 5521 5580 5581 5640 5641 5700 5701 5760 5761 5820 5821 5880 5881 5940 5941 6000 6001 6060 6061 6120 6121 6180 6181 6240 6241 6300 6301 6360 6361 6420 6421 6480 6481 6540 6541 6600 6601 6660 6661 6720 6721 6780 6781 6840 6841 6900 6901 6960 6961 7020 7021 7080 7081 7140 7141 7200 7201 7260 7261 7320 7321 7380 7381 7440 7441 7500 7501 7560 7561 7620 7621 7680 7681 7740 7741 7800 7801 7860 7861 7920 7921 7980 7981 8040 8041 8100 8101 8160 8161 8220 8221 8280 8281 8340 8341 8400 8401 8460 8461 8520 8521 8580 8581 8640 8641 8700 8701 8760 8761 8820 8821 8880 8881 8940 8941 9000 9001 9060 9061 9120 9121 9180 9181 9240 9241 9300 -Q1 18 -Q2 2 -P -T --keep-overhangs --x-raxml raxml --x-mafft mafft for file in RAxMLbestTree..tree; do mv "$file" "${file//RAxMLbestTree./ptyr2}" done for file in AlignedReads.fasta; do sed 's///' "$file" > "$file".sed mv "$file".sed "$file" done for file in AlignedReads.fasta; do mv "$file" "${file//AlignedReads/ptyr2_}" done mv ptyr2_tree "/work/or105/Gates_2014/2015_PANGEA_DualPairsFromFastQIVA/phylotypes" mv ptyr2*fasta "/work/or105/Gates_2014/2015_PANGEA_DualPairsFromFastQIVA/phylotypes" cd $CWD rm -r "$CWD/pty_16-01-20-13-35-09"
Fixed with latest commit
ChrisHIV
commented
8 years ago
Hi Chris, Running phylotype.py as below, I get the following error:
1 60 1 60 Traceback (most recent call last): File "/work/or105/libs/phylotypes/phylotypes.py", line 634, in
FirstSeq = str(AllSeqsToPrint[0].seq)
IndexError: list index out of range
Do you have an idea what s going on? Thanks! olli
!/bin/sh
PBS -l walltime=1:59:59,pcput=1:45:00
PBS -l select=1:ncpus=1:mem=3600mb
PBS -j oe
PBS -q pqeph
module load intel-suite/2015.1 mpi R/3.2.0 raxml/8.2.4 mafft/7 anaconda/2.3.0 samtools CWD=$(pwd) echo $CWD mkdir -p "$CWD/pty_16-01-20-13-35-09" cp "/work/or105/Gates_2014/2015_PANGEA_DualPairsFromFastQIVA/ptyruns/ptyr2_bam.txt" "$CWD/pty_16-01-20-13-35-09" cp "/work/or105/Gates_2014/2015_PANGEA_DualPairsFromFastQIVA/ptyruns/ptyr2_ref.txt" "$CWD/pty_16-01-20-13-35-09" cd "$CWD/pty_16-01-20-13-35-09" /work/or105/libs/phylotypes/phylotypes.py 3 2 "ptyr2_bam.txt" "ptyr2_ref.txt" 1 60 61 120 121 180 181 240 241 300 301 360 361 420 421 480 481 540 541 600 601 660 661 720 721 780 781 840 841 900 901 960 961 1020 1021 1080 1081 1140 1141 1200 1201 1260 1261 1320 1321 1380 1381 1440 1441 1500 1501 1560 1561 1620 1621 1680 1681 1740 1741 1800 1801 1860 1861 1920 1921 1980 1981 2040 2041 2100 2101 2160 2161 2220 2221 2280 2281 2340 2341 2400 2401 2460 2461 2520 2521 2580 2581 2640 2641 2700 2701 2760 2761 2820 2821 2880 2881 2940 2941 3000 3001 3060 3061 3120 3121 3180 3181 3240 3241 3300 3301 3360 3361 3420 3421 3480 3481 3540 3541 3600 3601 3660 3661 3720 3721 3780 3781 3840 3841 3900 3901 3960 3961 4020 4021 4080 4081 4140 4141 4200 4201 4260 4261 4320 4321 4380 4381 4440 4441 4500 4501 4560 4561 4620 4621 4680 4681 4740 4741 4800 4801 4860 4861 4920 4921 4980 4981 5040 5041 5100 5101 5160 5161 5220 5221 5280 5281 5340 5341 5400 5401 5460 5461 5520 5521 5580 5581 5640 5641 5700 5701 5760 5761 5820 5821 5880 5881 5940 5941 6000 6001 6060 6061 6120 6121 6180 6181 6240 6241 6300 6301 6360 6361 6420 6421 6480 6481 6540 6541 6600 6601 6660 6661 6720 6721 6780 6781 6840 6841 6900 6901 6960 6961 7020 7021 7080 7081 7140 7141 7200 7201 7260 7261 7320 7321 7380 7381 7440 7441 7500 7501 7560 7561 7620 7621 7680 7681 7740 7741 7800 7801 7860 7861 7920 7921 7980 7981 8040 8041 8100 8101 8160 8161 8220 8221 8280 8281 8340 8341 8400 8401 8460 8461 8520 8521 8580 8581 8640 8641 8700 8701 8760 8761 8820 8821 8880 8881 8940 8941 9000 9001 9060 9061 9120 9121 9180 9181 9240 9241 9300 -Q1 18 -Q2 2 -P -T --keep-overhangs --x-raxml raxml --x-mafft mafft for file in RAxMLbestTree..tree; do mv "$file" "${file//RAxMLbestTree./ptyr2}" done for file in AlignedReads.fasta; do sed 's///' "$file" > "$file".sed
mv "$file".sed "$file"
done
for file in AlignedReads .fasta; do
mv "$file" "${file//AlignedReads/ptyr2_}"
done
mv ptyr2_tree "/work/or105/Gates_2014/2015_PANGEA_DualPairsFromFastQIVA/phylotypes"
mv ptyr2*fasta "/work/or105/Gates_2014/2015_PANGEA_DualPairsFromFastQIVA/phylotypes"
cd $CWD
rm -r "$CWD/pty_16-01-20-13-35-09"