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chaeusler
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studyforrest-ppa-analysis
DOI
10.12751/g-node.7is9s6
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run-3_movie-ppa-grp.feat
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report_log.html

report_log.html 14 KB
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  1. <HTML><HEAD>
    2. 

  2. <!--refreshstart-->
    3. 

  3. 

  4. <!--refreshstop-->
    5. 

  5. <link REL=stylesheet TYPE=text/css href=.files/fsl.css>
    6. 

  6. <TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=report.html></OBJECT>
    7. 

  7. <h2>Progress Report / Log</h2>
    8. 

  8. Started at Fri 13 Mar 2020 11:08:15 PM CET<p>
    9. 

  9. Feat main script<br><pre>
    10. 

  10. 

  11. /bin/cp /data/project/studyforrest_ppa/sub-01/run-3_1st_movie-ppa-grp.fsf design.fsf
    12. 

  12. 

  13. /usr/share/fsl/5.0/bin/feat_model design
    14. 

  14. Warning: at least one EV is (close to) a linear combination of the others. You probably need to alter your design.
    15. 

  15. (Design matrix is rank deficient - ratio of min:max eigenvalues in SVD of matrix is 5.49306e-20)
    16. 

  16.  Contrasts involving these combinations will be set to zero.
    17. 

  17. 

  18. 

  19. mkdir .files;cp /usr/share/fsl/5.0/doc/fsl.css .files;cp -r /usr/share/fsl/5.0/doc/images .files/images
    20. 

  20. 

  21. /usr/share/fsl/5.0/bin/fsl_sub -T 10 -l logs -N feat0_init   /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-01/run-3_movie-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-01/run-3_movie-ppa-grp.feat -I 1 -init
    22. 

  22. 26683
    23. 

  23. 

  24. /usr/share/fsl/5.0/bin/fsl_sub -T 111 -l logs -N feat2_pre -j 26683  /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-01/run-3_movie-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-01/run-3_movie-ppa-grp.feat -I 1 -prestats
    25. 

  25. 27985
    26. 

  26. 

  27. /usr/share/fsl/5.0/bin/fsl_sub -T 200 -l logs -N feat3_film -j 27985  /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-01/run-3_movie-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-01/run-3_movie-ppa-grp.feat -I 1 -stats
    28. 

  28. 32620
    29. 

  29. 

  30. /usr/share/fsl/5.0/bin/fsl_sub -T 119 -l logs -N feat4_post -j 32620  /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-01/run-3_movie-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-01/run-3_movie-ppa-grp.feat -poststats 0 
    31. 

  31. couldn't open "tmpreport_poststats.html": no such file or directory
    32. 

  32.     while executing
    33. 

  33. "if { [ catch {
    34. 

  34. 

  35. for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
    36. 

  36.     switch -- [ lindex $argv $argindex ] {
    37. 

  37. 

  38. 	-I {
    39. 

  39. 	    incr arginde..."
    40. 

  40.     (file "/usr/share/fsl/5.0/bin/feat" line 309)
    41. 

  41. 

  42. FATAL ERROR ENCOUNTERED:
    43. 

  43. COMMAND:
    44. 

  44. /usr/share/fsl/5.0/bin/fsl_sub -T 119 -l logs -N feat4_post -j 32620  /usr/share/fsl/5.0/bin/feat /data/project/studyforrest_ppa/sub-01/run-3_movie-ppa-grp.feat/design.fsf -D /data/project/studyforrest_ppa/sub-01/run-3_movie-ppa-grp.feat -poststats 0 
    45. 

  45. ERROR MESSAGE:
    46. 

  46. child process exited abnormally
    47. 

  47. END OF ERROR MESSAGE
    48. 

  48. </pre><hr>Initialisation<br><pre>
    49. 

  49. 

  50. /usr/share/fsl/5.0/bin/fslmaths /data/project/studyforrest_ppa/inputs/studyforrest-data-aligned/sub-01/in_bold3Tp2/sub-01_task-avmovie_run-3_bold prefiltered_func_data -odt float
    51. 

  51. Total original volumes = 438
    52. 

  52. 

  53. /usr/share/fsl/5.0/bin/fslroi prefiltered_func_data example_func 219 1
    54. 

  54. </pre><hr>Preprocessing:Stage 1<br><pre>
    55. 

  55. </pre><hr>Preprocessing:Stage 2<br><pre>
    56. 

  56. 

  57. /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data -Tmean mean_func
    58. 

  58. 

  59. /usr/share/fsl/5.0/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/share/fsl/5.0/bin/immv mask_mask mask
    60. 

  60. 

  61. /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data -mas mask prefiltered_func_data_bet
    62. 

  62. 

  63. /usr/share/fsl/5.0/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
    64. 

  64. 0.000000 445.000000 
    65. 

  65. 

  66. /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_bet -thr 44.5 -Tmin -bin mask -odt char
    67. 

  67. 

  68. /usr/share/fsl/5.0/bin/fslstats prefiltered_func_data -k mask -p 50
    69. 

  69. 352.000000 
    70. 

  70. 

  71. /usr/share/fsl/5.0/bin/fslmaths mask -dilF mask
    72. 

  72. 

  73. /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data -mas mask prefiltered_func_data_thresh
    74. 

  74. 

  75. /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func
    76. 

  76. 

  77. /usr/share/fsl/5.0/bin/susan prefiltered_func_data_thresh 264.0 1.6985138004246285 3 1 1 mean_func 264.0 prefiltered_func_data_smooth
    78. 

  78. 

  79. /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth
    80. 

  80. 

  81. /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_smooth -mul 28.40909090909091 prefiltered_func_data_intnorm
    82. 

  82. 

  83. /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean
    84. 

  84. 

  85. /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_intnorm -bptf 37.49998125000937 -1 -add tempMean prefiltered_func_data_tempfilt
    86. 

  86. 

  87. /usr/share/fsl/5.0/bin/imrm tempMean
    88. 

  88. 

  89. /usr/share/fsl/5.0/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data
    90. 

  90. 

  91. /usr/share/fsl/5.0/bin/fslmaths filtered_func_data -Tmean mean_func
    92. 

  92. 

  93. /bin/rm -rf prefiltered_func_data*
    94. 

  94. </pre><hr>Stats<br><pre>
    95. 

  95. 

  96. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/avmovie/run-3/vse_new.txt custom_timing_files/ev1.txt
    97. 

  97. 

  98. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/avmovie/run-3/vse_old.txt custom_timing_files/ev2.txt
    99. 

  99. 

  100. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/avmovie/run-3/vlo_ch.txt custom_timing_files/ev3.txt
    101. 

  101. 

  102. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/avmovie/run-3/vpe_new.txt custom_timing_files/ev4.txt
    103. 

  103. 

  104. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/avmovie/run-3/vno_cut.txt custom_timing_files/ev6.txt
    105. 

  105. 

  106. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/aomovie/run-3/se_new.txt custom_timing_files/ev7.txt
    107. 

  107. 

  108. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/aomovie/run-3/se_old.txt custom_timing_files/ev8.txt
    109. 

  109. 

  110. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/avmovie/run-3/fg_av_ger_lr.txt custom_timing_files/ev9.txt
    111. 

  111. 

  112. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/avmovie/run-3/fg_av_ger_lrdiff.txt custom_timing_files/ev10.txt
    113. 

  113. 

  114. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/avmovie/run-3/fg_av_ger_ml.txt custom_timing_files/ev11.txt
    115. 

  115. 

  116. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/avmovie/run-3/fg_av_ger_pd.txt custom_timing_files/ev12.txt
    117. 

  117. 

  118. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/avmovie/run-3/fg_av_ger_rms.txt custom_timing_files/ev13.txt
    119. 

  119. 

  120. mkdir -p custom_timing_files ; /usr/share/fsl/5.0/bin/fslFixText /data/project/studyforrest_ppa/sub-01/onsets/avmovie/run-3/fg_av_ger_ud.txt custom_timing_files/ev14.txt
    121. 

  121. 

  122. paste -d  ' '  /data/project/studyforrest_ppa/inputs/studyforrest-data-aligned/sub-01/in_bold3Tp2/sub-01_task-avmovie_run-3_bold_mcparams.txt > confoundevs.txt
    123. 

  123. 

  124. /usr/share/fsl/5.0/bin/feat_model design confoundevs.txt
    125. 

  125. Warning: at least one EV is (close to) a linear combination of the others. You probably need to alter your design.
    126. 

  126. (Design matrix is rank deficient - ratio of min:max eigenvalues in SVD of matrix is 5.22927e-20)
    127. 

  127.  Contrasts involving these combinations will be set to zero.
    128. 

  128. 

  129. 

  130. /usr/share/fsl/5.0/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con  
    131. 

  131. Log directory is: stats
    132. 

  132. paradigm.getDesignMatrix().Nrows()=438
    133. 

  133. paradigm.getDesignMatrix().Ncols()=34
    134. 

  134. sizeTS=438
    135. 

  135. numTS=100410
    136. 

  136. Calculating residuals...
    137. 

  137. Completed
    138. 

  138. Estimating residual autocorrelation...
    139. 

  139. Calculating raw AutoCorrs... Completed
    140. 

  140. mode = 10088.5
    141. 

  141. sig = 905
    142. 

  142. Spatially smoothing auto corr estimates
    143. 

  143. ...................
    144. 

  144. Completed
    145. 

  145. Tukey M = 20
    146. 

  146. Tukey estimates... Completed
    147. 

  147. Completed
    148. 

  148. Prewhitening and Computing PEs...
    149. 

  149. Percentage done:
    150. 

  150. 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
    151. 

  151. Saving results... 
    152. 

  152. Completed
    153. 

  153. 

  154. /usr/share/fsl/5.0/bin/smoothest -d 404   -m mask -r stats/res4d > stats/smoothness
    155. 

  155. </pre><hr>Post-stats<br><pre>
    156. 

  156. 

  157. /usr/share/fsl/5.0/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1
    158. 

  158. 

  159. echo 100410 > thresh_zstat1.vol
    160. 

  160. zstat1: DLH=0.276768 VOLUME=100410 RESELS=16.6915
    161. 

  161. 

  162. /usr/share/fsl/5.0/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2
    163. 

  163. 

  164. echo 100410 > thresh_zstat2.vol
    165. 

  165. zstat2: DLH=0.276768 VOLUME=100410 RESELS=16.6915
    166. 

  166. 

  167. /usr/share/fsl/5.0/bin/fslmaths stats/zstat3 -mas mask thresh_zstat3
    168. 

  168. 

  169. echo 100410 > thresh_zstat3.vol
    170. 

  170. zstat3: DLH=0.276768 VOLUME=100410 RESELS=16.6915
    171. 

  171. 

  172. /usr/share/fsl/5.0/bin/fslmaths stats/zstat4 -mas mask thresh_zstat4
    173. 

  173. 

  174. echo 100410 > thresh_zstat4.vol
    175. 

  175. zstat4: DLH=0.276768 VOLUME=100410 RESELS=16.6915
    176. 

  176. 

  177. /usr/share/fsl/5.0/bin/fslmaths stats/zstat5 -mas mask thresh_zstat5
    178. 

  178. 

  179. echo 100410 > thresh_zstat5.vol
    180. 

  180. zstat5: DLH=0.276768 VOLUME=100410 RESELS=16.6915
    181. 

  181. 

  182. /usr/share/fsl/5.0/bin/fslmaths stats/zstat6 -mas mask thresh_zstat6
    183. 

  183. 

  184. echo 100410 > thresh_zstat6.vol
    185. 

  185. zstat6: DLH=0.276768 VOLUME=100410 RESELS=16.6915
    186. 

  186. 

  187. /usr/share/fsl/5.0/bin/fslmaths stats/zstat7 -mas mask thresh_zstat7
    188. 

  188. 

  189. echo 100410 > thresh_zstat7.vol
    190. 

  190. zstat7: DLH=0.276768 VOLUME=100410 RESELS=16.6915
    191. 

  191. 

  192. /usr/share/fsl/5.0/bin/fslmaths stats/zstat8 -mas mask thresh_zstat8
    193. 

  193. 

  194. echo 100410 > thresh_zstat8.vol
    195. 

  195. zstat8: DLH=0.276768 VOLUME=100410 RESELS=16.6915
    196. 

  196. 

  197. /usr/share/fsl/5.0/bin/fslmaths stats/zstat9 -mas mask thresh_zstat9
    198. 

  198. 

  199. echo 100410 > thresh_zstat9.vol
    200. 

  200. zstat9: DLH=0.276768 VOLUME=100410 RESELS=16.6915
    201. 

  201. 

  202. /usr/share/fsl/5.0/bin/fslmaths stats/zstat10 -mas mask thresh_zstat10
    203. 

  203. 

  204. echo 100410 > thresh_zstat10.vol
    205. 

  205. zstat10: DLH=0.276768 VOLUME=100410 RESELS=16.6915
    206. 

  206. 

  207. /usr/share/fsl/5.0/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.4 -p 0.05 -d 0.276768 --volume=100410 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26  --olmax=lmax_zstat1.txt --scalarname=Z > cluster_zstat1.txt
    208. 

  208. 

  209. /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat1 
    210. 

  210. 

  211. /usr/share/fsl/5.0/bin/cluster -i thresh_zstat2 -c stats/cope2 -t 3.4 -p 0.05 -d 0.276768 --volume=100410 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26  --olmax=lmax_zstat2.txt --scalarname=Z > cluster_zstat2.txt
    212. 

  212. 

  213. /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat2 
    214. 

  214. 

  215. /usr/share/fsl/5.0/bin/cluster -i thresh_zstat3 -c stats/cope3 -t 3.4 -p 0.05 -d 0.276768 --volume=100410 --othresh=thresh_zstat3 -o cluster_mask_zstat3 --connectivity=26  --olmax=lmax_zstat3.txt --scalarname=Z > cluster_zstat3.txt
    216. 

  216. 

  217. /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat3 
    218. 

  218. 

  219. /usr/share/fsl/5.0/bin/cluster -i thresh_zstat4 -c stats/cope4 -t 3.4 -p 0.05 -d 0.276768 --volume=100410 --othresh=thresh_zstat4 -o cluster_mask_zstat4 --connectivity=26  --olmax=lmax_zstat4.txt --scalarname=Z > cluster_zstat4.txt
    220. 

  220. 

  221. /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat4 
    222. 

  222. 

  223. /usr/share/fsl/5.0/bin/cluster -i thresh_zstat5 -c stats/cope5 -t 3.4 -p 0.05 -d 0.276768 --volume=100410 --othresh=thresh_zstat5 -o cluster_mask_zstat5 --connectivity=26  --olmax=lmax_zstat5.txt --scalarname=Z > cluster_zstat5.txt
    224. 

  224. 

  225. /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat5 
    226. 

  226. 

  227. /usr/share/fsl/5.0/bin/cluster -i thresh_zstat6 -c stats/cope6 -t 3.4 -p 0.05 -d 0.276768 --volume=100410 --othresh=thresh_zstat6 -o cluster_mask_zstat6 --connectivity=26  --olmax=lmax_zstat6.txt --scalarname=Z > cluster_zstat6.txt
    228. 

  228. 

  229. /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat6 
    230. 

  230. 

  231. /usr/share/fsl/5.0/bin/cluster -i thresh_zstat7 -c stats/cope7 -t 3.4 -p 0.05 -d 0.276768 --volume=100410 --othresh=thresh_zstat7 -o cluster_mask_zstat7 --connectivity=26  --olmax=lmax_zstat7.txt --scalarname=Z > cluster_zstat7.txt
    232. 

  232. 

  233. /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat7 
    234. 

  234. 

  235. /usr/share/fsl/5.0/bin/cluster -i thresh_zstat8 -c stats/cope8 -t 3.4 -p 0.05 -d 0.276768 --volume=100410 --othresh=thresh_zstat8 -o cluster_mask_zstat8 --connectivity=26  --olmax=lmax_zstat8.txt --scalarname=Z > cluster_zstat8.txt
    236. 

  236. 

  237. /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat8 
    238. 

  238. 

  239. /usr/share/fsl/5.0/bin/cluster -i thresh_zstat9 -c stats/cope9 -t 3.4 -p 0.05 -d 0.276768 --volume=100410 --othresh=thresh_zstat9 -o cluster_mask_zstat9 --connectivity=26  --olmax=lmax_zstat9.txt --scalarname=Z > cluster_zstat9.txt
    240. 

  240. 

  241. /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat9 
    242. 

  242. 

  243. /usr/share/fsl/5.0/bin/cluster -i thresh_zstat10 -c stats/cope10 -t 3.4 -p 0.05 -d 0.276768 --volume=100410 --othresh=thresh_zstat10 -o cluster_mask_zstat10 --connectivity=26  --olmax=lmax_zstat10.txt --scalarname=Z > cluster_zstat10.txt
    244. 

  244. 

  245. /usr/share/fsl/5.0/bin/cluster2html . cluster_zstat10 
    246. 

  246. 

  247. /usr/share/fsl/5.0/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null
    248. 

  248. 3.400654 5.394946 
    249. 

  249. 

  250. /usr/share/fsl/5.0/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null
    251. 

  251. 3.410028 6.963636 
    252. 

  252. 

  253. /usr/share/fsl/5.0/bin/fslstats thresh_zstat3 -l 0.0001 -R 2>/dev/null
    254. 

  254. 3.447011 6.922751 
    255. 

  255. 

  256. /usr/share/fsl/5.0/bin/fslstats thresh_zstat4 -l 0.0001 -R 2>/dev/null
    257. 

  257. 3.545249 6.077283 
    258. 

  258. 

  259. /usr/share/fsl/5.0/bin/fslstats thresh_zstat5 -l 0.0001 -R 2>/dev/null
    260. 

  260. 3.401183 5.522078 
    261. 

  261. 

  262. /usr/share/fsl/5.0/bin/fslstats thresh_zstat6 -l 0.0001 -R 2>/dev/null
    263. 

  263. 0.000000 0.000000 
    264. 

  264. 

  265. /usr/share/fsl/5.0/bin/fslstats thresh_zstat7 -l 0.0001 -R 2>/dev/null
    266. 

  266. 3.606698 7.633440 
    267. 

  267. 

  268. /usr/share/fsl/5.0/bin/fslstats thresh_zstat8 -l 0.0001 -R 2>/dev/null
    269. 

  269. 3.438692 6.983398 
    270. 

  270. 

  271. /usr/share/fsl/5.0/bin/fslstats thresh_zstat9 -l 0.0001 -R 2>/dev/null
    272. 

  272. 0.000000 0.000000 
    273. 

  273. 

  274. /usr/share/fsl/5.0/bin/fslstats thresh_zstat10 -l 0.0001 -R 2>/dev/null
    275. 

  275. 0.000000 0.000000 
    276. 

  276. Rendering using zmin=3.400654 zmax=7.633440
    277. 

  277. couldn't open "tmpreport_poststats.html": no such file or directory
    278. 

  278.     while executing
    279. 

  279. "if { [ catch {
    280. 

  280. 

  281. for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
    282. 

  282.     switch -- [ lindex $argv $argindex ] {
    283. 

  283. 

  284. 	-I {
    285. 

  285. 	    incr arginde..."
    286. 

  286.     (file "/usr/share/fsl/5.0/bin/feat" line 309)
    287. 

  287. Error encountered while running in main feat script, halting.
    288. 

  288. couldn't open "tmpreport_poststats.html": no such file or directory
    289. 

  289. </pre><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br></BODY></HTML>
    290.