[galaxy-dev] Error running oasesoptimizer rev. 53e887dda799 (konradpaszkiewicz) on Galaxy fd4113962c32+ (stable)

Hi, Regarding the error I experienced with [galaxy-dev] Error running oasesoptimizer rev. 53e887dda799 (konradpaszkiewicz) on Galaxy fd4113962c32+ (stable) Two things: FIRST The error I reported, in short, it was my fault as I failed to to set up the: cmdline = '/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.sh %s %s \'%s\' %s %s 2&1>/dev/null' line properly in the oases_optimiser.py script properly I guess it would help for developers to state exactly the customization required for each package installed via ToolShed for the tool to work properly or better yet, it would be really nice if we could set up environmental variables like: TOOL_SHED_REPOS=/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos so that scripts could invoke them upon installation: cmdline = '$TOOL_SHED_REPOS/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.sh %s %s \'%s\' %s %s 2&1>/dev/null' SECOND I still am experiencing errors with this tool When I run oases_optimiser on either fasta or fastq files the jobs start, run and then fail In all cases the problem is the lack of an ''splicing_events.txt' file Help will be appreciated Thanks --R ##### The stderr is as follows: Traceback (most recent call last): File "/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py", line 120, in <module> if __name__ == "__main__": __main__() File "/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py", line 76, in __main__ for line in open(path ): IOError: [Errno 2] No such file or directory: 'splicing_events.txt' ##### The stdout is as follows: [0.000000] Reading FastQ file /usr/local/galaxy/galaxy-dist/database/files/003/dataset_3687.dat; [13.354877] 8855297 sequences found [13.354879] Done [13.354940] Reading read set file ./Sequences; [14.405160] 8855297 sequences found [20.956147] Done [20.956153] 8855297 sequences in total. [20.956229] Writing into roadmap file ./Roadmaps... [23.008558] Inputting sequences... [23.008571] Inputting sequence 0 / 8855297 [25.835351] Inputting sequence 1000000 / 8855297 [28.835964] Inputting sequence 2000000 / 8855297 [31.938277] Inputting sequence 3000000 / 8855297 [35.129436] Inputting sequence 4000000 / 8855297 [38.384093] Inputting sequence 5000000 / 8855297 [41.660153] Inputting sequence 6000000 / 8855297 [44.905326] Inputting sequence 7000000 / 8855297 [48.168615] Inputting sequence 8000000 / 8855297 [50.969068] === Sequences loaded in 28.188442 s [50.969101] Done inputting sequences [50.969103] Destroying splay table [51.018112] Splay table destroyed [0.000000] Reading roadmap file ./Roadmaps [13.140830] 8855297 roadmaps read [13.144978] Creating insertion markers [15.796233] Ordering insertion markers [21.652798] Counting preNodes [22.631404] 2753107 preNodes counted, creating them now [24.516794] Sequence 1000000 / 8855297 [25.609456] Sequence 2000000 / 8855297 [26.585862] Sequence 3000000 / 8855297 [27.501523] Sequence 4000000 / 8855297 [28.375045] Sequence 5000000 / 8855297 [29.217391] Sequence 6000000 / 8855297 [30.037355] Sequence 7000000 / 8855297 [30.838062] Sequence 8000000 / 8855297 [31.514315] Adjusting marker info... [32.498044] Connecting preNodes [32.734023] Connecting 1000000 / 8855297 [33.029694] Connecting 2000000 / 8855297 [33.360000] Connecting 3000000 / 8855297 [33.712200] Connecting 4000000 / 8855297 [34.080947] Connecting 5000000 / 8855297 [34.464629] Connecting 6000000 / 8855297 [34.853754] Connecting 7000000 / 8855297 [35.256476] Connecting 8000000 / 8855297 [35.604610] Cleaning up memory [35.622205] Done creating preGraph [35.622208] Concatenation... [36.944164] Renumbering preNodes [36.944174] Initial preNode count 2753107 [36.992738] Destroyed 2139761 preNodes [36.992745] Concatenation over! [36.992747] Clipping short tips off preGraph [37.241017] Concatenation... [37.561728] Renumbering preNodes [37.561735] Initial preNode count 613346 [37.564816] Destroyed 602327 preNodes [37.564818] Concatenation over! [37.564819] 565869 tips cut off [37.564820] 11019 nodes left [37.564908] Writing into pregraph file ./PreGraph... [37.628994] Reading read set file ./Sequences; [38.666026] 8855297 sequences found [45.262765] Done [47.287358] Reading pre-graph file ./PreGraph [47.287449] Graph has 11019 nodes and 8855297 sequences [47.320337] Scanning pre-graph file ./PreGraph for k-mers [47.345965] 587492 kmers found [47.410094] Sorting kmer occurence table ... [47.807351] Sorting done. [47.807356] Computing acceleration table... [47.839961] Computing offsets... [47.856571] Ghost Threading through reads 0 / 8855297 [49.327252] Ghost Threading through reads 1000000 / 8855297 [50.789941] Ghost Threading through reads 2000000 / 8855297 [52.251861] Ghost Threading through reads 3000000 / 8855297 [53.719122] Ghost Threading through reads 4000000 / 8855297 [55.175811] Ghost Threading through reads 5000000 / 8855297 [56.640149] Ghost Threading through reads 6000000 / 8855297 [58.103628] Ghost Threading through reads 7000000 / 8855297 [59.570354] Ghost Threading through reads 8000000 / 8855297 [60.865193] === Ghost-Threaded in 13.008623 s [60.865203] Threading through reads 0 / 8855297 [62.545417] Threading through reads 1000000 / 8855297 [64.224281] Threading through reads 2000000 / 8855297 [65.912903] Threading through reads 3000000 / 8855297 [67.591620] Threading through reads 4000000 / 8855297 [69.271917] Threading through reads 5000000 / 8855297 [70.956665] Threading through reads 6000000 / 8855297 [72.633673] Threading through reads 7000000 / 8855297 [74.323969] Threading through reads 8000000 / 8855297 [75.752202] === Threaded in 14.886999 s [76.213422] Correcting graph with cutoff 0.200000 [76.215727] Determining eligible starting points [76.223605] Done listing starting nodes [76.223606] Initializing todo lists [76.224193] Done with initilization [76.224195] Activating arc lookup table [76.224796] Done activating arc lookup table [76.246815] 10000 / 11019 nodes visited [76.247077] Concatenation... [76.247364] Renumbering nodes [76.247365] Initial node count 11019 [76.247654] Removed 140 null nodes [76.247655] Concatenation over! [76.247655] Clipping short tips off graph, drastic [76.251632] Concatenation... [76.363538] Renumbering nodes [76.363546] Initial node count 10879 [76.363860] Removed 3988 null nodes [76.363861] Concatenation over! [76.363862] 6891 nodes left [76.363931] Writing into graph file ./Graph2... [77.954766] WARNING: NO COVERAGE CUTOFF PROVIDED [77.954770] Velvet will probably leave behind many detectable errors [77.954771] See manual for instructions on how to set the coverage cutoff parameter [77.954779] Removing contigs with coverage < -1.000000... [77.959164] Concatenation... [77.959591] Renumbering nodes [77.959591] Initial node count 6891 [77.959603] Removed 0 null nodes [77.959604] Concatenation over! [77.959817] Concatenation... [77.959947] Renumbering nodes [77.959947] Initial node count 6891 [77.959958] Removed 0 null nodes [77.959958] Concatenation over! [77.959962] Clipping short tips off graph, drastic [77.960338] Concatenation... [77.960467] Renumbering nodes [77.960468] Initial node count 6891 [77.960479] Removed 0 null nodes [77.960479] Concatenation over! [77.960479] 6891 nodes left [77.960481] WARNING: NO EXPECTED COVERAGE PROVIDED [77.960481] Velvet will be unable to resolve any repeats [77.960481] See manual for instructions on how to set the expected coverage parameter [77.960482] Concatenation... [77.960610] Renumbering nodes [77.960610] Initial node count 6891 [77.960621] Removed 0 null nodes [77.960621] Concatenation over! [77.960622] Removing reference contigs with coverage < -1.000000... [77.960918] Concatenation... [77.961047] Renumbering nodes [77.961047] Initial node count 6891 [77.961058] Removed 0 null nodes [77.961059] Concatenation over! [78.028474] Writing contigs into ./contigs.fa... [79.423669] Writing into stats file ./stats.txt... [79.559581] Writing into graph file ./LastGraph... Final graph has 6891 nodes and n50 of 96, max 2769, total 569496, using 5202858/8855297 reads [0.000000] Reading graph file ./Graph2 [0.000070] Graph has 6891 nodes and 8855297 sequences [2.414712] Reading read set file ./Sequences; [3.454420] 8855297 sequences found [9.983101] Done [12.073890] Removing contigs with coverage < 3.000000... [12.077227] Concatenation... [12.110841] Renumbering nodes [12.110844] Initial node count 6891 [12.111045] Removed 112 null nodes [12.111046] Concatenation over! [12.111295] Concatenation... [12.111423] Renumbering nodes [12.111423] Initial node count 6779 [12.111436] Removed 0 null nodes [12.111436] Concatenation over! [12.111441] Clipping short tips off graph, drastic [12.112174] Concatenation... [12.112311] Renumbering nodes [12.112312] Initial node count 6779 [12.112405] Removed 7 null nodes [12.112406] Concatenation over! [12.112406] 6772 nodes left [12.112407] Correcting graph with cutoff 0.200000 [12.112413] Removing low coverage edges from the graph [12.116981] Concatenation... [12.205746] Renumbering nodes [12.205752] Initial node count 6772 [12.205956] Removed 32 null nodes [12.205957] Concatenation over! [12.206236] Determining eligible starting points [12.209874] Done listing starting nodes [12.209876] Initializing todo lists [12.210092] Done with initilization [12.210092] Activating arc lookup table [12.210256] Done activating arc lookup table [12.211125] 1000 nodes visited [12.211314] 2000 nodes visited [12.211725] 3000 nodes visited [12.211981] 4000 nodes visited [12.212184] 5000 nodes visited [12.212412] 6000 nodes visited [12.212988] 7000 nodes visited [12.214581] 8000 nodes visited [12.214905] 9000 nodes visited [12.215178] 10000 nodes visited [12.215483] 11000 nodes visited [12.215855] 12000 nodes visited [12.216435] 13000 nodes visited [12.217246] Concatenation... [12.239617] Renumbering nodes [12.239620] Initial node count 6740 [12.239808] Removed 78 null nodes [12.239809] Concatenation over! [12.239810] Clipping short tips off graph, drastic [12.240542] Concatenation... [12.269659] Renumbering nodes [12.269667] Initial node count 6662 [12.269860] Removed 21 null nodes [12.269861] Concatenation over! [12.269861] 6641 nodes left [12.269863] Removing low coverage edges from the graph [12.270134] Concatenation... [12.270253] Renumbering nodes [12.270254] Initial node count 6641 [12.270266] Removed 0 null nodes [12.270267] Concatenation over! [12.270750] Writing into stats file ./stats.txt... [12.418659] Writing into graph file ./LastGraph... Computing local connections [18.310196] Activating arc lookup table [18.310878] Done activating arc lookup table Extracting loci from connection graph... [18.532657] Counted 3577 mRNA loci Transitive reduction of graph Preparing to correct graph with cutoff 0.200000 Deactivating local correction settings Preparing to correct graph with cutoff 0.200000 Deactivating local correction settings [18.623163] Exporting transcripts to ./transcripts.fa [18.637751] Exporting transcript contigs to ./contig-ordering.txt [18.773863] Finished extracting transcripts, used 4747390/8855297 reads [0.000000] Reading FastQ file /usr/local/galaxy/galaxy-dist/database/files/003/dataset_3687.dat; [12.768650] 8855297 sequences found [12.768653] Done [12.945838] Reading read set file ./Sequences; [13.863345] 8855297 sequences found [19.497520] Done [19.497531] 8855297 sequences in total. [19.541544] Writing into roadmap file ./Roadmaps... [21.360277] Inputting sequences... [21.360288] Inputting sequence 0 / 8855297 [23.204556] Inputting sequence 1000000 / 8855297 [25.109676] Inputting sequence 2000000 / 8855297 [27.073594] Inputting sequence 3000000 / 8855297 [29.074912] Inputting sequence 4000000 / 8855297 [31.101859] Inputting sequence 5000000 / 8855297 [33.295043] Inputting sequence 6000000 / 8855297 [35.624233] Inputting sequence 7000000 / 8855297 [37.969184] Inputting sequence 8000000 / 8855297 [39.983558] === Sequences loaded in 18.844462 s [40.106935] Done inputting sequences [40.106938] Destroying splay table [40.147227] Splay table destroyed [0.000000] Reading roadmap file ./Roadmaps [10.688511] 8855297 roadmaps read [10.694034] Creating insertion markers [12.646929] Ordering insertion markers [16.397709] Counting preNodes [17.105913] 1802122 preNodes counted, creating them now [18.580180] Sequence 1000000 / 8855297 [19.551491] Sequence 2000000 / 8855297 [20.443988] Sequence 3000000 / 8855297 [21.288288] Sequence 4000000 / 8855297 [22.100638] Sequence 5000000 / 8855297 [22.889490] Sequence 6000000 / 8855297 [23.659644] Sequence 7000000 / 8855297 [24.414121] Sequence 8000000 / 8855297 [25.053583] Adjusting marker info... [25.710606] Connecting preNodes [25.814606] Connecting 1000000 / 8855297 [25.936316] Connecting 2000000 / 8855297 [26.072741] Connecting 3000000 / 8855297 [26.215108] Connecting 4000000 / 8855297 [26.368631] Connecting 5000000 / 8855297 [26.522818] Connecting 6000000 / 8855297 [26.681469] Connecting 7000000 / 8855297 [26.845782] Connecting 8000000 / 8855297 [26.987872] Cleaning up memory [27.003705] Done creating preGraph [27.003708] Concatenation... [27.767289] Renumbering preNodes [27.767294] Initial preNode count 1802122 [27.793408] Destroyed 1115129 preNodes [27.793419] Concatenation over! [27.793421] Clipping short tips off preGraph [27.933941] Concatenation... [27.943271] Renumbering preNodes [27.943273] Initial preNode count 686993 [27.946796] Destroyed 685336 preNodes [27.946798] Concatenation over! [27.946799] 676719 tips cut off [27.946799] 1657 nodes left [27.946865] Writing into pregraph file ./PreGraph... [27.958115] Reading read set file ./Sequences; [29.008103] 8855297 sequences found [35.730429] Done [37.535139] Reading pre-graph file ./PreGraph [37.750964] Graph has 1657 nodes and 8855297 sequences [37.755970] Scanning pre-graph file ./PreGraph for k-mers [37.774919] 85345 kmers found [37.784901] Sorting kmer occurence table ... [37.821440] Sorting done. [37.821442] Computing acceleration table... [37.839000] Computing offsets... [37.841254] Ghost Threading through reads 0 / 8855297 [38.725065] Ghost Threading through reads 1000000 / 8855297 [39.601268] Ghost Threading through reads 2000000 / 8855297 [40.473358] Ghost Threading through reads 3000000 / 8855297 [41.347286] Ghost Threading through reads 4000000 / 8855297 [42.220368] Ghost Threading through reads 5000000 / 8855297 [43.096893] Ghost Threading through reads 6000000 / 8855297 [43.969893] Ghost Threading through reads 7000000 / 8855297 [44.844439] Ghost Threading through reads 8000000 / 8855297 [45.596543] === Ghost-Threaded in 7.755290 s [45.596549] Threading through reads 0 / 8855297 [46.518374] Threading through reads 1000000 / 8855297 [47.444445] Threading through reads 2000000 / 8855297 [48.366937] Threading through reads 3000000 / 8855297 [49.288411] Threading through reads 4000000 / 8855297 [50.211439] Threading through reads 5000000 / 8855297 [51.138604] Threading through reads 6000000 / 8855297 [52.061485] Threading through reads 7000000 / 8855297 [52.985071] Threading through reads 8000000 / 8855297 [53.776191] === Threaded in 8.179642 s [54.119435] Correcting graph with cutoff 0.200000 [54.119719] Determining eligible starting points [54.120670] Done listing starting nodes [54.120672] Initializing todo lists [54.120754] Done with initilization [54.120755] Activating arc lookup table [54.120825] Done activating arc lookup table [54.123725] Concatenation... [54.123766] Renumbering nodes [54.123766] Initial node count 1657 [54.123811] Removed 12 null nodes [54.123812] Concatenation over! [54.123813] Clipping short tips off graph, drastic [54.124252] Concatenation... [54.224979] Renumbering nodes [54.224989] Initial node count 1645 [54.225027] Removed 685 null nodes [54.225028] Concatenation over! [54.225029] 960 nodes left [54.225116] Writing into graph file ./Graph2... [55.367296] WARNING: NO COVERAGE CUTOFF PROVIDED [55.367299] Velvet will probably leave behind many detectable errors [55.367299] See manual for instructions on how to set the coverage cutoff parameter [55.367310] Removing contigs with coverage < -1.000000... [55.369762] Concatenation... [55.369800] Renumbering nodes [55.369800] Initial node count 960 [55.369804] Removed 0 null nodes [55.369804] Concatenation over! [55.369836] Concatenation... [55.369852] Renumbering nodes [55.369852] Initial node count 960 [55.369854] Removed 0 null nodes [55.369855] Concatenation over! [55.369859] Clipping short tips off graph, drastic [55.369917] Concatenation... [55.369933] Renumbering nodes [55.369933] Initial node count 960 [55.369935] Removed 0 null nodes [55.369936] Concatenation over! [55.369936] 960 nodes left [55.369937] WARNING: NO EXPECTED COVERAGE PROVIDED [55.369938] Velvet will be unable to resolve any repeats [55.369938] See manual for instructions on how to set the expected coverage parameter [55.369939] Concatenation... [55.369955] Renumbering nodes [55.369955] Initial node count 960 [55.369957] Removed 0 null nodes [55.369958] Concatenation over! [55.369958] Removing reference contigs with coverage < -1.000000... [55.370004] Concatenation... [55.370020] Renumbering nodes [55.370020] Initial node count 960 [55.370023] Removed 0 null nodes [55.370023] Concatenation over! [55.422086] Writing contigs into ./contigs.fa... [56.445270] Writing into stats file ./stats.txt... [56.509837] Writing into graph file ./LastGraph... Final graph has 960 nodes and n50 of 97, max 2466, total 83275, using 3349500/8855297 reads [0.000000] Reading graph file ./Graph2 [0.000036] Graph has 960 nodes and 8855297 sequences [1.504128] Reading read set file ./Sequences; [2.507512] 8855297 sequences found [9.014853] Done [11.103883] Removing contigs with coverage < 3.000000... [11.106359] Concatenation... [11.106391] Renumbering nodes [11.106392] Initial node count 960 [11.106405] Removed 0 null nodes [11.106406] Concatenation over! [11.106437] Concatenation... [11.106451] Renumbering nodes [11.106452] Initial node count 960 [11.106454] Removed 0 null nodes [11.106454] Concatenation over! [11.106457] Clipping short tips off graph, drastic [11.106511] Concatenation... [11.106526] Renumbering nodes [11.106526] Initial node count 960 [11.106528] Removed 0 null nodes [11.106529] Concatenation over! [11.106529] 960 nodes left [11.106530] Correcting graph with cutoff 0.200000 [11.106533] Removing low coverage edges from the graph [11.107536] Concatenation... [11.143393] Renumbering nodes [11.143395] Initial node count 960 [11.143419] Removed 2 null nodes [11.143420] Concatenation over! [11.143472] Determining eligible starting points [11.143963] Done listing starting nodes [11.143965] Initializing todo lists [11.143992] Done with initilization [11.143993] Activating arc lookup table [11.144018] Done activating arc lookup table [11.144227] 1000 nodes visited [11.144573] Concatenation... [11.170620] Renumbering nodes [11.170625] Initial node count 958 [11.170649] Removed 3 null nodes [11.170650] Concatenation over! [11.170650] Clipping short tips off graph, drastic [11.170755] Concatenation... [11.170770] Renumbering nodes [11.170770] Initial node count 955 [11.170777] Removed 1 null nodes [11.170777] Concatenation over! [11.170778] 954 nodes left [11.170778] Removing low coverage edges from the graph [11.170807] Concatenation... [11.170821] Renumbering nodes [11.170822] Initial node count 954 [11.170824] Removed 0 null nodes [11.170825] Concatenation over! [11.170964] Writing into stats file ./stats.txt... [11.230812] Writing into graph file ./LastGraph... Computing local connections [14.746804] Activating arc lookup table [14.746902] Done activating arc lookup table Extracting loci from connection graph... [14.901713] Counted 680 mRNA loci Transitive reduction of graph Preparing to correct graph with cutoff 0.200000 Deactivating local correction settings Preparing to correct graph with cutoff 0.200000 Deactivating local correction settings [14.943051] Exporting transcripts to ./transcripts.fa [14.945550] Exporting transcript contigs to ./contig-ordering.txt [15.018696] Finished extracting transcripts, used 2812567/8855297 reads [0.000000] Reading FastA file transcripts_19.fa; [0.010226] 1570 sequences found [0.010227] Done [0.010247] Reading FastA file transcripts_21.fa; [0.011900] 344 sequences found [0.011901] Done [0.011933] Reading FastQ file /usr/local/galaxy/galaxy-dist/database/files/003/dataset_3687.dat; [12.198483] 8855297 sequences found [12.198486] Done [12.401859] Reading read set file ./Sequences; [13.230828] 8857211 sequences found [18.721759] Done [18.721771] 8857211 sequences in total. [18.757685] Writing into roadmap file ./Roadmaps... [20.584822] Inputting sequences... [20.584833] Inputting sequence 0 / 8857211 [22.366728] Inputting sequence 1000000 / 8857211 [24.064109] Inputting sequence 2000000 / 8857211 [25.810546] Inputting sequence 3000000 / 8857211 [27.594079] Inputting sequence 4000000 / 8857211 [29.489010] Inputting sequence 5000000 / 8857211 [31.550585] Inputting sequence 6000000 / 8857211 [33.630592] Inputting sequence 7000000 / 8857211 [35.727077] Inputting sequence 8000000 / 8857211 [37.556610] === Sequences loaded in 17.186429 s [37.658648] Done inputting sequences [37.658651] Destroying splay table [37.699062] Splay table destroyed [0.000000] Reading roadmap file ./Roadmaps [9.685475] 8857211 roadmaps read [9.691067] Creating insertion markers [10.875179] Ordering insertion markers [15.994335] Counting preNodes [16.591386] 1819394 preNodes counted, creating them now [18.120056] Sequence 1000000 / 8857211 [19.096796] Sequence 2000000 / 8857211 [20.019315] Sequence 3000000 / 8857211 [20.903522] Sequence 4000000 / 8857211 [21.760984] Sequence 5000000 / 8857211 [22.597284] Sequence 6000000 / 8857211 [23.416069] Sequence 7000000 / 8857211 [24.216209] Sequence 8000000 / 8857211 [24.899732] Adjusting marker info... [25.431336] Connecting preNodes [25.558999] Connecting 1000000 / 8857211 [25.675256] Connecting 2000000 / 8857211 [25.804199] Connecting 3000000 / 8857211 [25.937344] Connecting 4000000 / 8857211 [26.076245] Connecting 5000000 / 8857211 [26.221485] Connecting 6000000 / 8857211 [26.374118] Connecting 7000000 / 8857211 [26.527566] Connecting 8000000 / 8857211 [26.663482] Cleaning up memory [26.676121] Done creating preGraph [26.676124] Concatenation... [27.334684] Renumbering preNodes [27.334691] Initial preNode count 1819394 [27.360193] Destroyed 1162378 preNodes [27.360203] Concatenation over! [27.360204] Clipping short tips off preGraph [27.472827] Concatenation... [27.482889] Renumbering preNodes [27.482890] Initial preNode count 657016 [27.486213] Destroyed 654610 preNodes [27.486215] Concatenation over! [27.486215] 642103 tips cut off [27.486216] 2406 nodes left [27.486304] Writing into pregraph file ./PreGraph... [27.632873] Reading read set file ./Sequences; [28.652946] 8857211 sequences found [35.138336] Done [36.942242] Reading pre-graph file ./PreGraph [37.162349] Graph has 2406 nodes and 8857211 sequences [37.177742] Scanning pre-graph file ./PreGraph for k-mers [37.202831] 323188 kmers found [37.235987] Sorting kmer occurence table ... [37.412622] Sorting done. [37.412631] Computing acceleration table... [37.436981] Computing offsets... [37.446554] Ghost Threading through reads 0 / 8857211 [38.426036] Ghost Threading through reads 1000000 / 8857211 [39.403194] Ghost Threading through reads 2000000 / 8857211 [40.382459] Ghost Threading through reads 3000000 / 8857211 [41.359848] Ghost Threading through reads 4000000 / 8857211 [42.338263] Ghost Threading through reads 5000000 / 8857211 [43.312651] Ghost Threading through reads 6000000 / 8857211 [44.288659] Ghost Threading through reads 7000000 / 8857211 [45.262101] Ghost Threading through reads 8000000 / 8857211 [46.097808] === Ghost-Threaded in 8.651254 s [46.097819] Threading through reads 0 / 8857211 [47.257090] Threading through reads 1000000 / 8857211 [48.297172] Threading through reads 2000000 / 8857211 [49.336488] Threading through reads 3000000 / 8857211 [50.376047] Threading through reads 4000000 / 8857211 [51.415893] Threading through reads 5000000 / 8857211 [52.455649] Threading through reads 6000000 / 8857211 [53.494621] Threading through reads 7000000 / 8857211 [54.534154] Threading through reads 8000000 / 8857211 [55.426228] === Threaded in 9.328408 s [55.878521] Correcting graph with cutoff 0.200000 [55.878882] Determining eligible starting points [55.880237] Done listing starting nodes [55.880238] Initializing todo lists [55.880345] Done with initilization [55.880346] Activating arc lookup table [55.880433] Done activating arc lookup table [55.882259] Concatenation... [55.882315] Renumbering nodes [55.882316] Initial node count 2406 [55.882381] Removed 8 null nodes [55.882391] Concatenation over! [55.882391] Clipping short tips off graph, drastic [55.883006] Concatenation... [55.986679] Renumbering nodes [55.986689] Initial node count 2398 [55.986751] Removed 757 null nodes [55.986752] Concatenation over! [55.986753] 1641 nodes left [55.986847] Writing into graph file ./Graph2... [57.586219] WARNING: NO COVERAGE CUTOFF PROVIDED [57.586222] Velvet will probably leave behind many detectable errors [57.586223] See manual for instructions on how to set the coverage cutoff parameter [57.586229] Removing contigs with coverage < -1.000000... [57.588755] Concatenation... [57.588822] Renumbering nodes [57.588823] Initial node count 1641 [57.588828] Removed 0 null nodes [57.588828] Concatenation over! [57.588882] Concatenation... [57.588910] Renumbering nodes [57.588910] Initial node count 1641 [57.588914] Removed 0 null nodes [57.588914] Concatenation over! [57.588918] Clipping short tips off graph, drastic [57.589010] Concatenation... [57.589038] Renumbering nodes [57.589038] Initial node count 1641 [57.589042] Removed 0 null nodes [57.589042] Concatenation over! [57.589043] 1641 nodes left [57.589044] WARNING: NO EXPECTED COVERAGE PROVIDED [57.589044] Velvet will be unable to resolve any repeats [57.589045] See manual for instructions on how to set the expected coverage parameter [57.589046] Concatenation... [57.589073] Renumbering nodes [57.589074] Initial node count 1641 [57.589077] Removed 0 null nodes [57.589077] Concatenation over! [57.589078] Removing reference contigs with coverage < -1.000000... [57.589313] Concatenation... [57.589342] Renumbering nodes [57.589343] Initial node count 1641 [57.589346] Removed 0 null nodes [57.589347] Concatenation over! [57.642005] Writing contigs into ./contigs.fa... [59.115401] Writing into stats file ./stats.txt... [59.194880] Writing into graph file ./LastGraph... Final graph has 1641 nodes and n50 of 253, max 2780, total 321253, using 4663132/8857211 reads [0.000000] Reading graph file ./Graph2 [0.000035] Graph has 1641 nodes and 8857211 sequences [2.107753] Reading read set file ./Sequences; [3.038393] 8857211 sequences found [9.441180] Done [11.533317] Removing contigs with coverage < 3.000000... [11.536633] Concatenation... [11.536765] Renumbering nodes [11.536766] Initial node count 1641 [11.536809] Removed 38 null nodes [11.536810] Concatenation over! [11.536862] Concatenation... [11.536889] Renumbering nodes [11.536889] Initial node count 1603 [11.536892] Removed 0 null nodes [11.536893] Concatenation over! [11.536896] Clipping short tips off graph, drastic [11.536986] Concatenation... [11.537012] Renumbering nodes [11.537013] Initial node count 1603 [11.537016] Removed 0 null nodes [11.537017] Concatenation over! [11.537017] 1603 nodes left [11.537018] Correcting graph with cutoff 0.200000 [11.537021] Removing low coverage edges from the graph [11.537755] Concatenation... [11.570878] Renumbering nodes [11.570880] Initial node count 1603 [11.570922] Removed 2 null nodes [11.570923] Concatenation over! [11.570992] Determining eligible starting points [11.571857] Done listing starting nodes [11.571859] Initializing todo lists [11.571906] Done with initilization [11.571907] Activating arc lookup table [11.571953] Done activating arc lookup table [11.572158] 1000 nodes visited [11.572367] 2000 nodes visited [11.572720] 3000 nodes visited [11.574751] Concatenation... [11.658520] Renumbering nodes [11.658526] Initial node count 1601 [11.658573] Removed 13 null nodes [11.658575] Concatenation over! [11.658576] Clipping short tips off graph, drastic [11.658669] Concatenation... [11.658696] Renumbering nodes [11.658696] Initial node count 1588 [11.658699] Removed 0 null nodes [11.658700] Concatenation over! [11.658700] 1588 nodes left [11.658701] Removing low coverage edges from the graph [11.658754] Concatenation... [11.658779] Renumbering nodes [11.658779] Initial node count 1588 [11.658783] Removed 0 null nodes [11.658783] Concatenation over! [11.659006] Writing into stats file ./stats.txt... [11.739723] Writing into graph file ./LastGraph... Computing local connections [16.410447] Activating arc lookup table [16.410585] Done activating arc lookup table Extracting loci from connection graph... [16.589680] Counted 1507 mRNA loci Transitive reduction of graph Preparing to correct graph with cutoff 0.200000 Deactivating local correction settings Preparing to correct graph with cutoff 0.200000 Deactivating local correction settings [16.653772] Exporting transcripts to ./transcripts.fa [16.668614] Exporting transcript contigs to ./contig-ordering.txt [16.783990] Finished extracting transcripts, used 4672425/8857211 reads [16.787745] Printing unused reads into ./UnusedReads.fa [24.411594] Writing into AMOS file ./oases_asm.afg... Thanks Again --R