Activity for Francesco Cicconardi
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Francesco Cicconardi posted a comment on ticket #29
Hi, This is the new log. ESC[0;35m###### Wed Apr 22 05:43:48 BST 2020: Running layoutESC[0m INPUT reads lis mates PLACEMENT CONFLICT ASSEMBLY OUTPUT ESC[0;35m###### Sun Apr 26 17:18:38 BST 2020: Running consensusESC[0m Entering 'Amos_supercontigs.bnk' Found CTG bank unlocking 'r 432968 tk19812' Found FRG bank Found LAY bank Found LIB bank Found RED bank Found SCF bank Found UNV bank IFOs found: 7 File locks: 0 Bank locks: 1 Starting on Sun Apr 26 17:18:38 2020 Read bank is Amos_supercontigs.bnk Alignment...
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I'm suspecting it's a memory issue. Is there any chance I can split the delta file to run part of that and reconnect them after? Cheers F
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Now I don't have it anymore, but the log file was just listing the different stages of the job like: INPUT reads lis ... till the end without returning any expicit error. F
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Hi, I think consensus fails because layout didn't generate the file. layout also finishes without error messages Thanks a lot F
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casm-layout ERROR
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Hi Pasi, Thanks for your help. Apparently the small change in the assembly generated a mis-joining in the LM. I'm sure probably to a repeat region in those flanking areas. One scaffolder was able to solve it the other not. I also used the good LM to break down scaffolds, re-scaffold and gap filling them, re compute che LM and use it fo a final scaffolding. Now it looks really good. A final gap filling closed most of the LM gaps. Now I should be quite happy with it. As I'm not familiar with the sensitivity...
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Hi Pasi, I'm having a problem with the linkadge map. The fist run produced a satisfied result, but, for reason that I'm not explaining here I went back to my assembly and I build a different version of the draft using a different software to perform the scaffolding. I then generated the LM for the new assembly version and the draft before the scaffolding. Comparing the 3 LMs it seems like the draft and the second scaffolding procedure produced comparable results which prodced worst results than the...
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Ok, will do it. Is it in LMPlot section of your wiki? Something to mention is that AllMaps found this ambiguities: 11:26:59 [__init__] CACHEDIR=/home/fc464/.cache/matplotlib 11:26:59 [font_manager] Using fontManager instance from /home/fc464/.cache/matplotlib/fontList.json 11:26:59 [__init__] backend agg version v2.2 11:26:59 [base] Load file `../EisaPacBio.LMmale.bed` 11:27:02 [allmaps] Map contains 184033 markers in 31 linkage groups. 11:27:03 [allmaps] Retained 162,372 of 184,033 (88.2%) clean...
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Ok, will do it. Something to mention is that AllMaps found this ambiguities: 11:26:59 [__init__] CACHEDIR=/home/fc464/.cache/matplotlib 11:26:59 [font_manager] Using fontManager instance from /home/fc464/.cache/matplotlib/fontList.json 11:26:59 [__init__] backend agg version v2.2 11:26:59 [base] Load file `../EisaPacBio.LMmale.bed` 11:27:02 [allmaps] Map contains 184033 markers in 31 linkage groups. 11:27:03 [allmaps] Retained 162,372 of 184,033 (88.2%) clean markers. 11:27:03 [base] Load file `weights.txt`...
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Hi Pasi, I rerun the step using lodLimit=14 sizeLimit=100 maleTheta=0.05 femaleTheta=0 I decided to set femaleTheta to 0 because in lepidoptera the recombination in females is not present. The distribution I have now for the LGs is better: 341 33 741 32 2363 31 2383 30 3166 29 3319 28 3386 27 3781 26 4014 25 4067 24 4329 23 4675 22 4706 21 4887 20 5160 19 5187 18 5462 17 6038 16 6123 15 6157 14 6166 13 6413 12 7040 11 7163 10 7470 9 7478 8 7791 7 7954 6 8317 5 8533 4 9938 3 10058 2 10509 1 264007...
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I increased the lodLimit to 15, now I got this Number of LGs = 74, markers in LGs = 172849, singles = 276273 2157 30 2942 29 2945 28 3057 27 3198 26 3648 25 3770 24 3818 23 4081 22 4347 21 4609 20 4727 19 4763 18 5127 17 5497 16 5688 15 5744 14 5808 13 6080 12 6451 11 6615 10 7026 9 7098 8 7386 7 7420 6 7875 5 8139 4 9143 3 9564 2 9831 1 276273 0 I'm also changing Theta values as maleTheta=0.05 femaleTheta=0. Am I dong it wrong? F
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Dear Pasi, it seems like there's something wrong here. The size distribution of the best 31 linkage groups: #Markers LG 10 13 10 134 10 17 10 2202 10 23 10 35 10 55 10 559 10 65 10 88 11 14 11 21 11 29 11 37 11 52 11 545 11 7 11 8 12 4 12 41 12 9 13 24 13 27 13 58 14 158 14 5 14 6 15 3 25 2 87122 0 350773 1 not very well distributed F
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In that file there are 3357 values in the first column, some have a value on the next column, I'm guessing that those are my linkage groups and they og from 0 to 3357. I guess I have to use this sintax for OrderMarkers2: chromosome=0..3357, or should I rather use chromosome=1..31, because I know there are 31 chrs? How do I then know where the markers in the output file sits on in my scaffolds. Overall the whole process it's not very clear to me, would you be a little bit more explanatory, please....
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Can I do it in one run or it's one run for each scaffold? F
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Dear P, I'm using 32 cpus. I re run it with 3 iteration and with -Xmx128g, it finished. What is the parameter chromosome you're mentioning? I actually have only scaffolds and I need the linkagemap to run the scaffolding with AllMaps. About that I still need to figure out a way to convert the Lap-MAP LM into a suitable format for AllMaps, some details are listed here. Can you help me with that too? Cheers, F
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This is the command line zcat $PREFIX.post.call.filtered.gz | java -cp $LepMAP3modules/bin OrderMarkers2 map=$PREFIX.post.call.filtered.map5.js.txt data=- numThreads=$THREADS > $PREFIX.post.call.filtered.map5.js.OrderMarkers.it3.txt F Il giorno mar 16 apr 2019 alle ore 09:45 Pasi Rastas lep-map@users.sourceforge.net ha scritto: Dear F, Can you give the OrderMarkers2 command? Have you tried to re-run it or give more memory to java (-Xmx)? Cheers, Pasi Pipeline for Lep-MAP3 https://sourceforge.net/p/lep-map3/discussion/general/thread/a45e4cf0a2/?limit=25&page=1#a77e...
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This is the command line zcat $PREFIX.post.call.filtered.gz | java -cp $LepMAP3modules/bin OrderMarkers2 \ map=$PREFIX.post.call.filtered.map5.js.txt data=- \ numThreads=$THREADS > $PREFIX.post.call.filtered.map5.js.OrderMarkers.it3.txt F Il giorno mar 16 apr 2019 alle ore 09:45 Pasi Rastas lep-map@users.sourceforge.net ha scritto: Dear F, Can you give the OrderMarkers2 command? Have you tried to re-run it or give more memory to java (-Xmx)? Cheers, Pasi Pipeline for Lep-MAP3 https://sourceforge.net/p/lep-map3/discussion/general/thread/a45e4cf0a2/?limit=25&page=1#a77e...
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Hi Pasi, It's several days now that I'm trying to run OrderMarkers2 but it looks like it freezes. The cpus seem to run but the log freezes for days. Are you aware of this? What I should do? Usually it stops at the iteration 4. Thanks F
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Hi Pasi, It's several days now that I'm trying to run OrderMarkers2 but it looks like it freezes. The cpus seem to run but the log freezes for days. Are you aware of this? What I should do? Usually it stops at the iteration 4. Thanks F Il giorno ven 5 apr 2019 alle ore 10:10 Pasi Rastas lep-map@users.sourceforge.net ha scritto: Dear Francesco, Your map file has something strange in it (parameter map=file). Please check the file for line "�G�\��ɮ�<�&���" , encoding etc. I have got some reports earlier...
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I got an error with the new pedigree at the JoinSingles2All step ###### Thu 4 Apr 13:44:26 BST 2019: 1. Run mpileup + pileupParser2 + pileup2posterior pipe PileupParser2 parameters: limit1=3 limit2=24.3 limit3=8.1 limit4=170.1 Number of bams = 81 Number of individuals = 81 [mpileup] 81 samples in 81 input files ###### Thu 4 Apr 18:44:27 BST 2019: 2. Run ParentCall2 No grandparents present in family F1 Warning: Different number of grandparents (0 and 2) in family F2 Found 2 grandparents in family...
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Shell I run everything with default parameters? How many iterations for ordermarkers2? F On Thu, 4 Apr 2019, 11:36 Pasi Rastas, lep-map@users.sourceforge.net wrote: Seems ok, Cheers, Pasi Half-sib mapping with only a known mother and no grandparental information https://sourceforge.net/p/lep-map3/discussion/general/thread/6d0c01ad/?limit=25#e20e Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/lep-map3/discussion/general/ To unsubscribe from further messages,...
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Is this log means that I did it right? ###### Thu 4 Apr 10:33:45 BST 2019: 2. Run ParentCall2 No grandparents present in family F1 Warning: Different number of grandparents (0 and 2) in family F2 Found 2 grandparents in family F2 Number of individuals = 88 Number of families = 2 F Il giorno mer 3 apr 2019 alle ore 08:43 Pasi Rastas lep-map@users.sourceforge.net ha scritto: Searching for "grandparents" :) https://sourceforge.net/p/lep-map3/discussion/general/thread/885598e615/ Half-sib mapping with...
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Is this log means that I did it right? Thu 4 Apr 10:33:45 BST 2019: 2. Run ParentCall2 No grandparents present in family F1 Warning: Different number of grandparents (0 and 2) in family F2 Found 2 grandparents in family F2 Number of individuals = 88 Number of families = 2 F Il giorno mer 3 apr 2019 alle ore 08:43 Pasi Rastas lep-map@users.sourceforge.net ha scritto: Searching for "grandparents" :) https://sourceforge.net/p/lep-map3/discussion/general/thread/885598e615/ Half-sib mapping with only...
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That was just a test to check for errors. See the latest post. It's running with 82 samples. F On Tue, 2 Apr 2019, 07:53 Pasi Rastas, lep-map@users.sourceforge.net wrote: Dear F, As you have only 5 individuals, the mapping does not make much sense. No markers have been put to linkage groups. Number of individuals = 5 excluding grandparents Number of LGs = 0, markers in LGs = 0, singles = 8419 Cheers, Pasi Pipeline for Lep-MAP3 https://sourceforge.net/p/lep-map3/discussion/general/thread/a45e4cf0a2/?limit=25#cfa1...
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How? And, according to the other thread, which would be the parameters to be more of less stringent, especially in the filtering process. Now it's running the last step with no errors. I'll then just need to figure out how to convert it for AllMaps Thanks a lot!!! F On Tue, 2 Apr 2019, 07:51 Pasi Rastas, lep-map@users.sourceforge.net wrote: Yes, You can just add the grandparents to the pedigree for corresponding families and parents. Cheers, Pasi Half-sib mapping with only a known mother and no grandparental...
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Fix it!
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I rerun the analysis with the new pedigree. It work pretty much all the way down. I still have that error at JoinSingles2All ###### Mon 1 Apr 17:34:20 BST 2019: 2. Run ParentCall2 No grandparents present in family F1 No grandparents present in family F2 Number of individuals = 84 Number of families = 2 Number of called markers = 450479 (450479 informative) Number of called Z/X markers = 0 ###### Mon 1 Apr 17:57:19 BST 2019: 3. Filtering2 chi^2 limits are 10.8271484375, 13.8154296875, 16.265625 No...
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Now it says No grandparents present in family F1 No grandparents present in family F2 Number of individuals = 84 Number of families = 2 by actually grandparents for family F2 exists! F
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Ok, now I see. I thought I needed to keep the parents of the F2 parents. Great! Now I'll give it a try! Thanks a lot F
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Here the pedigree file and the pedigree tree F
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Hi Pasi, I thing my pedigree.txt is not well formatted. Would you please check it. As soon as the pedigree.txt contains the F2 family I got the error. And if I put F1 in all fields I get Error: Too many parents in a family F1 Please help F
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Hi Pasi, So, does it means I have to split the Run mpileup + pileupParser2 + pileup2posterior pipe file? I generate it with mpileup, then add the missing parents with 1s and run the pileupParser2 + pileup2posterior? F
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I can do that, but still JoinSingles2All fails ###### Fri 29 Mar 16:04:16 GMT 2019: 3. Filtering2 chi^2 limits are 10.8271484375, 13.8154296875, 16.265625 No grandparents present in family F1 Number of individuals = 5 Number of families = 1 Number of markers = 8419 ###### Fri 29 Mar 16:04:16 GMT 2019: 4. SeparateChromosomes2 Loading file No grandparents present in family F1 Number of individuals = 5 Number of families = 1 File loaded with 8419 SNPs Number of individuals = 5 excluding grandparents...
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but there's still the error afterwards F On Thu, 21 Mar 2019, 08:01 Pasi Rastas, lep-map@users.sourceforge.net wrote: Dear F, Yes, one parent is enough. Cheers, Pasi Pipeline for Lep-MAP3 https://sourceforge.net/p/lep-map3/discussion/general/thread/a45e4cf0a2/?limit=25#cf15 Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/lep-map3/discussion/general/ To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
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Hi Pasi, Apparently both parents are needed? ParentCall2 is complaining... Error: No parent(s) in a family F2 F
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Hi Pasi, While the mapping is running I thought to start preparing the follow up pipeline. Reading the documentation I came up with this. Is it correct? What are the parameters I can play with in order to be more or less stringent, and how can I convert the ordered map to use it with AllMaps? Thanks a lot! F samtools mpileup -q 10 -Q 10 -s $(cat sorted_bams) | awk -f $LepMAP3modules/pileupParser2.awk | awk -f $LepMAP3modules/pileup2posterior.awk | gzip > $ASSEMBLY.RADseq.post.gz $HOME/software/Lep-MAP3/transpose_tab...
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Hi Pasi, While the mapping is running I thought to start preparing the follow up pipeline. Reading the documentation I came up with this. Is it correct? What are the parameters I can play with in order to be more or less stringent, and how can I convert the ordered map to use it with AllMaps? Thanks a lot! F samtools mpileup -q 10 -Q 10 -s $(cat sorted_bams) | awk -f $LepMAP3modules/pileupParser2.awk | awk -f $LepMAP3modules/pileup2posterior.awk | gzip > $ASSEMBLY.RADseq.post.gz $HOME/software/Lep-MAP3/transpose_tab...
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I got an error Error 520 Error: No parent(s) in a family F1 What's wrong with my pedigree? This is part of the file CHR POS F1 F1 F1 F1 ... CHR POS EisaMC14-04 EisaMC14-11 EisaMC14-202 EisaMC14-131 ... CHR POS 0 0 MC14-04 MC14-04 ... CHR POS 0 0 MC14-11 MC14-11 ... CHR POS 1 2 1 1 ... CHR POS 0 0 0 0 ... What am I doing wrong? Thanks F
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I just executed samtools mpileup -q 10 -Q 10 -s $(cat sorted_bams) | awk -f $LepMAP3modules/pileupParser2.awk | awk -f $LepMAP3modules/pileup2posterior.awk on 81 sam files, why it says only 79 samples? it is referred to the offspring? Number of bams = 81 Number of individuals = 81 PileupParser2 parameters: limit1=3 limit2=24.3 limit3=8.1 limit4=170.1 [mpileup] 79 samples in 81 input files F
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Hi Pasi, Sorry to bother you again. Still about the pedigree file. Shell I put 0 in the 4th line if I don't have that parent right? and, the family name of the F1 and F2 should be different or the same? Thanks a lot!!! F
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Do I always need the two parents? What if I have only one? F On Wed, 20 Mar 2019, 17:41 Pasi Rastas, lep-map@users.sourceforge.net wrote: Great, you can analyse the data together as 7 or 8 families. You can and should include F0 (grandparents), F1 (parents) and F2 individuals. You can also include F0 + F1 as own family. The two offspring family might be too small... Cheers, Pasi Pipeline for Lep-MAP3 https://sourceforge.net/p/lep-map3/discussion/general/thread/a45e4cf0a2/?limit=25#9755 Sent from...
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Hi Pasi, Here is the pedegree. Shell I use only the F1 or I can use the F2 individuals? Thanks F
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I think I found what I needed!!! the 2 parents and 78 offspring. Good enough? F
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Thanks Pasi, I'll see what I can do F
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Hi Pasi I presume your library contains several F1:s as I downloaded the data from a published paper I guess it is a pool of individuals. Do I need the separate them somehow, or the can stay pooled together in the same fastq file? Thanks a lot for your help F
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Hi everyone, I'm new to likadge maps, I haven't anything before. I'm struggling to understand what I need to do and how to produce an input file for AllMaps. What I have is a reference genome that I wanto to scaffold using the map and 3 RAD-seq libraries, a father, a mother and 1 offspring (F1). I have no problem in mapping reads. From this point on I'm pretty much lost. I was trying to follow the documentation running samtools mpileup in pipe with pileupParser2.awk and pileup2posterior.awk samtools...
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