Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates a consensus tree. It plots the maximum likelihood tree with bootstrap values, drift and residuals and calculates statistics for every migration event, such as migration support, standard error and p-values.
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Issue with Treemix v 1.13, error occurs when using the -tf parameter to specify .newick #17
Dear,
I have run the Step3_TreeMix.sh, and generated the "_finalconstree.newick", like "(((((((Sample1:1000.0,(((((Sample2:1000.0,Sample3:1000.0):368.0,Sample4:1000.0):693.0,Sample5:1000.0):242.0,(Sample6:1000.0,Sample7:1000.0):92.0):338.0,Sample8:1000.0):182.0):125.0,Sample9:1000.0):54.0,(Sample10:1000.0,Sample11:1000.0):27.0):1.00,((Sample12:1000.0,Sample13:1000.0):41.0,(Sample14:1000.0,Sample15:1000.0):28.0):1.00,(Sample16:1000.0,Sample17:1000.0):54.0,((Sample18:1000.0,Sample19:1000.0):52.0,(Sample20:1000.0,Sample21:1000.0):44.0):1.00,((Sample22:1000.0,Sample23:1000.0):45.0,(Sample24:1000.0,Sample25:1000.0):33.0):1.00,(Sample26:1000.0,Sample27:1000.0):34.0,(Sample28:1000.0,Sample29:1000.0):38.0,(Sample30:1000.0,Sample31:1000.0):43.0,((Sample32:1000.0,Sample33:1000.0):41.0,(Sample34:1000.0,Sample35:1000.0):33.0):1.00,(Sample36:1000.0,Sample37:1000.0):37.0):1.00,(Sample38:1000.0,Sample39:1000.0):38.0):40.0,Sample40:1000.0):1000.0,Sample41:1000.0);
', but when I directed further run ""treemix -i $1 -k $3 -global -m $6 -root $4 -tf $4"_finalconstree.newick" -o "finalruns/"$4$6"mfinalrun"$1"" using newick file generated from previous step, error occurs like "/var/spool/slurm/slurmd/job03945/slurm_script: line 45: 20221 Segmentation fault (core dumped)... ". I speculated it was a problem with the newick format, so I imported the newick file into Mega and regenerated it without support value, like "(((((((((((((((Sample1,(((((Sample2,Sample3),Sample4),Sample5),(Sample6,Sample7)),Sample8)),Sample9),(Sample10,Sample11)),((Sample12,Sample13),(Sample14,Sample15))),(Sample16,Sample17)),((Sample18,Sample19),(Sample20,Sample21))),((Sample22,Sample23),(Sample24,Sample25))),(Sample26,Sample27)),(Sample28,Sample29)),(Sample30,Sample31)),((Sample32,Sample33),(Sample34,Sample35))),(Sample36,Sample37)),(Sample38,Sample39)),Sample40),Sample41);". However, when I used this newick file, program seems to be running normally, but the result file has not been generated yet, and it has been running for 2 days so far. So I would like to ask, is it normal for the program to run for such a long time? Or perhaps there is another issue with the newick file format.
Dear, I have run the Step3_TreeMix.sh, and generated the "_finalconstree.newick", like "(((((((Sample1:1000.0,(((((Sample2:1000.0,Sample3:1000.0):368.0,Sample4:1000.0):693.0,Sample5:1000.0):242.0,(Sample6:1000.0,Sample7:1000.0):92.0):338.0,Sample8:1000.0):182.0):125.0,Sample9:1000.0):54.0,(Sample10:1000.0,Sample11:1000.0):27.0):1.00,((Sample12:1000.0,Sample13:1000.0):41.0,(Sample14:1000.0,Sample15:1000.0):28.0):1.00,(Sample16:1000.0,Sample17:1000.0):54.0,((Sample18:1000.0,Sample19:1000.0):52.0,(Sample20:1000.0,Sample21:1000.0):44.0):1.00,((Sample22:1000.0,Sample23:1000.0):45.0,(Sample24:1000.0,Sample25:1000.0):33.0):1.00,(Sample26:1000.0,Sample27:1000.0):34.0,(Sample28:1000.0,Sample29:1000.0):38.0,(Sample30:1000.0,Sample31:1000.0):43.0,((Sample32:1000.0,Sample33:1000.0):41.0,(Sample34:1000.0,Sample35:1000.0):33.0):1.00,(Sample36:1000.0,Sample37:1000.0):37.0):1.00,(Sample38:1000.0,Sample39:1000.0):38.0):40.0,Sample40:1000.0):1000.0,Sample41:1000.0); ', but when I directed further run ""treemix -i $1 -k $3 -global -m $6 -root $4 -tf $4"_finalconstree.newick" -o "finalruns/"$4$6"mfinalrun"$1"" using newick file generated from previous step, error occurs like "/var/spool/slurm/slurmd/job03945/slurm_script: line 45: 20221 Segmentation fault (core dumped)... ". I speculated it was a problem with the newick format, so I imported the newick file into Mega and regenerated it without support value, like "(((((((((((((((Sample1,(((((Sample2,Sample3),Sample4),Sample5),(Sample6,Sample7)),Sample8)),Sample9),(Sample10,Sample11)),((Sample12,Sample13),(Sample14,Sample15))),(Sample16,Sample17)),((Sample18,Sample19),(Sample20,Sample21))),((Sample22,Sample23),(Sample24,Sample25))),(Sample26,Sample27)),(Sample28,Sample29)),(Sample30,Sample31)),((Sample32,Sample33),(Sample34,Sample35))),(Sample36,Sample37)),(Sample38,Sample39)),Sample40),Sample41);". However, when I used this newick file, program seems to be running normally, but the result file has not been generated yet, and it has been running for 2 days so far. So I would like to ask, is it normal for the program to run for such a long time? Or perhaps there is another issue with the newick file format.
Thanks!