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running the arg-sample:"error: cannot write 'arg-sample.0.smc.gz' " and " segment error " #33

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yangwukaidi opened this issue Oct 16, 2023 · 0 comments

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@yangwukaidi
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Hi, mdrasmus.
When running arg-sample, I encountered an error.
The error occurred after adding all the haploids and before the MSMC iteration, "error: cannot write 'arg-sample.0.smc.gz' " and " segment error "appeared in the error message. When I try again with data from other chromosomes, I get a similar error: "error: cannot write 'arg-sample.0.smc.gz' ".
This is the command line I used.
arg-sample -s LG01.sites --popsize 1000000 -r 1.5e-8 -m 2.5e-8 -c 5 --ntimes 20 --maxtime 1e6 --randomize-phase 1.0 --unphased --sample-phase 10 --resample-window-iters 1 --resample-window 10000 -n 1000

The following is the running process and the error.
add sequence 48 of 48 (Z-DHS8A_2)
treemap = 47 41
forward (423 states, 1097390 blocks): 18.0 m
trace: 1.8 m
sample_phase 5 4 size=149839 frac_switch=0.292441
add thread: 1.5 m

prior: -17362425.072964
likelihood: -81283502.965746
joint: -98645928.038711
nrecombs: 1113701
noncompats: 363109
arglen: 49808425453171.289062
max memory: 40345.7 MB

Climb Search (0 iterations)

prior: -17362425.072964
likelihood: -81283502.965746
joint: -98645928.038711
nrecombs: 1113701
noncompats: 363109
arglen: 49808425453171.289062
max memory: 40345.7 MB

error: cannot write 'arg-sample.0.smc.gz'
Resample All Branches (1000 iterations)

sample 1
treemap = 11 42
段错误(吐核)

After trying again, the run process and error are returned as follows:
add sequence 48 of 48 (QBZ-BCS1_1)
treemap = 47 27
forward (262 states, 2170225 blocks): 37.3 m
trace: 3.9 m
sample_phase 14 15 size=293816 frac_switch=0.258543
add thread: 3.1 m

prior: -34490254.623572
likelihood: -169762634.305310
joint: -204252888.928882
nrecombs: 2203306
noncompats: 732993
arglen: 99628066086952.109375
max memory: 83008.1 MB

Climb Search (0 iterations)

prior: -34490254.623572
likelihood: -169762634.305310
joint: -204252888.928882
nrecombs: 2203306
noncompats: 732993
arglen: 99628066086952.109375
max memory: 83008.1 MB

error: cannot write 'arg-sample.0.smc.gz'
Resample All Branches (1000 iterations)

sample 1
treemap = 14 29
*** Error in `arg-sample': double free or corruption (out): 0x00000002d150a370 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x7f465cdb6329]
arg-sample[0x40f8bd]
arg-sample[0x411724]
arg-sample[0x442b64]
arg-sample[0x439381]
arg-sample[0x42e862]
arg-sample[0x42ff67]
arg-sample[0x41ee26]
arg-sample[0x41ef0e]
arg-sample[0x45b5ee]
arg-sample[0x403b38]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f465cd57555]
arg-sample[0x4040d4]
======= Memory map: ========
00400000-00474000 r-xp 00000000 fd:02 1614423228 /home/user/anaconda3/envs/argw27/bin/arg-sample
00673000-00674000 r--p 00073000 fd:02 1614423228 /home/user/anaconda3/envs/argw27/bin/arg-sample
00674000-0067b000 rw-p 00074000 fd:02 1614423228 /home/user/anaconda3/envs/argw27/bin/arg-sample
015ed000-1949fe3000 rw-p 00000000 00:00 0 [heap]
7f4588000000-7f4588021000 rw-p 00000000 00:00 0
7f4588021000-7f458c000000 ---p 00000000 00:00 0
7f458ce93000-7f4593673000 rw-p 00000000 00:00 0
7f45938da000-7f45a66dc000 rw-p 00000000 00:00 0
7f45a7403000-7f45b1e8e000 rw-p 00000000 00:00 0
7f45b2954000-7f45b9e54000 rw-p 00000000 00:00 0
7f45bc64e000-7f45be5c1000 rw-p 00000000 00:00 0
7f45c0534000-7f45c247f000 rw-p 00000000 00:00 0
7f45c43ca000-7f465482c000 rw-p 00000000 00:00 0
7f46554f2000-7f465c431000 rw-p 00000000 00:00 0
7f465cd35000-7f465cef9000 r-xp 00000000 fd:00 33629431 /usr/lib64/libc-2.17.so
7f465cef9000-7f465d0f8000 ---p 001c4000 fd:00 33629431 /usr/lib64/libc-2.17.so
7f465d0f8000-7f465d0fc000 r--p 001c3000 fd:00 33629431 /usr/lib64/libc-2.17.so
7f465d0fc000-7f465d0fe000 rw-p 001c7000 fd:00 33629431 /usr/lib64/libc-2.17.so
7f465d0fe000-7f465d103000 rw-p 00000000 00:00 0
7f465d103000-7f465d118000 r-xp 00000000 fd:00 33558756 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f465d118000-7f465d317000 ---p 00015000 fd:00 33558756 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f465d317000-7f465d318000 r--p 00014000 fd:00 33558756 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f465d318000-7f465d319000 rw-p 00015000 fd:00 33558756 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f465d319000-7f465d41a000 r-xp 00000000 fd:00 33630259 /usr/lib64/libm-2.17.so
7f465d41a000-7f465d619000 ---p 00101000 fd:00 33630259 /usr/lib64/libm-2.17.so
7f465d619000-7f465d61a000 r--p 00100000 fd:00 33630259 /usr/lib64/libm-2.17.so
7f465d61a000-7f465d61b000 rw-p 00101000 fd:00 33630259 /usr/lib64/libm-2.17.so
7f465d61b000-7f465d704000 r-xp 00000000 fd:00 33669790 /usr/lib64/libstdc++.so.6.0.19
7f465d704000-7f465d904000 ---p 000e9000 fd:00 33669790 /usr/lib64/libstdc++.so.6.0.19
7f465d904000-7f465d90c000 r--p 000e9000 fd:00 33669790 /usr/lib64/libstdc++.so.6.0.19
7f465d90c000-7f465d90e000 rw-p 000f1000 fd:00 33669790 /usr/lib64/libstdc++.so.6.0.19
7f465d90e000-7f465d923000 rw-p 00000000 00:00 0
7f465d923000-7f465d945000 r-xp 00000000 fd:00 33629425 /usr/lib64/ld-2.17.so
7f465db26000-7f465db2b000 rw-p 00000000 00:00 0
7f465db3f000-7f465db44000 rw-p 00000000 00:00 0
7f465db44000-7f465db45000 r--p 00021000 fd:00 33629425 /usr/lib64/ld-2.17.so
7f465db45000-7f465db46000 rw-p 00022000 fd:00 33629425 /usr/lib64/ld-2.17.so
7f465db46000-7f465db47000 rw-p 00000000 00:00 0
7ffeb0f05000-7ffeb0f2d000 rw-p 00000000 00:00 0 [stack]
7ffeb0fc7000-7ffeb0fc9000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
已放弃(吐核)

How can I solve this problem?

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