crash everytime

[ch8316f5eyu]

I assemble mouse genome with nanopore long reads, but crash every time and I cannot figure out the reason. There is the error message:

`Fri Jun 19 09:20:34 CST 2020 MAP RAW READS TO ASSEMBLY

Fri Jun 19 09:53:52 CST 2020 WRITE GAP/CTGEND MATCHING RAW READS TO FILES

Fri Jun 19 09:58:39 CST 2020 RUN LOCAL ASSEMBLIES

Error in `/home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns': free(): corrupted unsorted chunks: 0x00000000017deda0 Error in `/home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns': free(): corrupted unsorted chunks: 0x0000000001d91da0 ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f50427fe7e5] /lib/x86_64-linux-gnu/libc.so.6/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f504280737a] /lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f188afa737a] /lib/x86_64-linux-gnu/libpthread.so.0(+0x76ba)[0x7f5042d726ba] /lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f188afab53c] /home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns[0x404415] /home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns[0x4036e1] /lib/x86_64-linux-gnu/libc.so.6(clone/lib/x86_64-linux-gnu/libpthread.so.0(+0x76ba)[0x7f188b5126ba] 00400000-00421000 r-xp 00000000 08:41 2139283 /home/yu/app/CSA2.6/bin/wtdbg2.2/wtdbg-cns 00620000-00621000 r--p 00020000 08:41 2139283 /home/yu/app/CSA2.6/bin/wtdbg2.2/wtdbg-cns 00621000-00622000 rw-p 00021000 08:41 2139283 /home/yu/app/CSA2.6/bin/wtdbg2.2/wtdbg-cns 017de000-01889000 rw-p 00000000 00:00 0 [heap] 7f502c000000-7f502c023000 rw-p 00000000 00:00 0` Maybe my RAM is too low(188G)? If it is the reason, I think you should mention the minimal RAW requirement. Thank you!

[HMPNK]

Hi,

this could be the few core dumps during the gap reassembly mentioned on the github CSA start page:

"You may see a few "core dumps", these are single gap re-assembly jobs that failed, you should just not care. Some gap re-assembly jobs may run very long due to huge read pile ups in that location, therefore we force gap re-assemblies to stop after 20 minutes using "timeout"."

You can just keep the tool running, it should finish with good results. If the pipeline really stops, post a list (ls -lhtr) of the 03_.... directory here, please. Also post the commandline you used to start CSA and the full log file

[HMPNK]

What type of reads are you using (technology/N50 readlength/coverage)?

[HMPNK]

And yes, 188Gb RAM is pretty low for a mammalian genome assembly, but I would expect a crash or infinite runtime earlier in the pipeline! I think you may need about 512Gb. We wrote this in the publication and on the github CSA start page:

"We show that CSA is able to produce chromosomal-level assemblies for smaller vertebrate genomes (fishes, birds) within 12 h on low-cost computing equipment ($1,000–2,000, Intel i7, 128 GB RAM), using just long-read data and a diverged reference genome (divergence time ∼65 million years ago [Mya]) as input. Larger mammalian genomes, such as human, can be assembled within 16 h on server equipment (Intel Xeon, 1 TB RAM)."

[ch8316f5eyu]

There is the command line: ~/app/CSA2.6/CSA2.6c.pl -r fastq/terc_Control.fa.gz -g ../../Reference/Genome_data/mm10/mm10.fa -t 10 -o N33 -d CSA > script/CAS.sh There is the output massage: `Sat Jun 20 07:27:21 CST 2020 RUN WTDBG on ../../fastq/terc_Control.fa.gz

Sat Jun 20 09:18:50 CST 2020 CREATE CONSENSUS / use wtdbg-cns

Sat Jun 20 12:12:18 CST 2020 COMPARE ASSEMBLIES AND SPLIT CONTIGS AT DIFFERENCES

Sat Jun 20 12:32:11 CST 2020 ASSEMBLY IMPROVEMENTS BY READ RE-MAPPING AND SPLITTING

PRIMARY CONTIG STATS: Total: 2422821200 Count: 7188 Average: 337064.72 Median: 72201 N00: 13324505 1 N10: 4195572 45 N20: 3071029 112 N30: 2312588 203 N40: 1751953 324 N50: 1279915 489 N60: 919184 714 N70: 650348 1027 N80: 413460 1489 N90: 188768 2346 N100: 2011 7188

Sat Jun 20 13:16:46 CST 2020 FINISHED CSA STEP1 real 349m25.456s user 3062m38.996s sys 76m49.160s

Sat Jun 20 13:16:47 CST 2020 MASKING REFERENCE BY SELF-ALIGNMENT

Sat Jun 20 14:45:43 CST 2020 CREATE LAST DATABASE FOR WHOLE GENOME ALIGNMENT

Sat Jun 20 15:01:03 CST 2020 RUN WHOLE GENOME ALIGNMENT BY LAST

Sat Jun 20 16:56:09 CST 2020 RUN RAGOUT TO ORDER CONTIGS ACCORDING TO REFERENCE

PRIMARY SCAFFOLD STATS: Total: 2506267816 Count: 1458 Average: 1718976.55 Median: 13842 N00: 188292983 1 N10: 174131707 2 N20: 166547346 3 N30: 146728522 5 N40: 143279141 7 N50: 125013353 9 N60: 119070898 11 N70: 111949287 13 N80: 106031649 15 N90: 88708220 18 N100: 2011 1458

Sat Jun 20 17:04:33 CST 2020 FINISHED CSA STEP2

real 227m45.360s user 1036m24.456s sys 138m14.948s

Sat Jun 20 17:04:56 CST 2020 MAP RAW READS TO ASSEMBLY

Sat Jun 20 17:22:07 CST 2020 WRITE GAP/CTGEND MATCHING RAW READS TO FILES

Sat Jun 20 17:25:35 CST 2020 RUN LOCAL ASSEMBLIES

Error in `/home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns': free(): corrupted unsorted chunks: 0x0000000000ca4da0 ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fb2657ca7e5] /lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7fb2657d337a] /lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7fb2657d753c] /home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns[0x404415] /home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns[0x4036e1] /lib/x86_64-linux-gnu/libpthread.so.0(+0x76ba)[0x7fb265d3e6ba] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7fb26585a41d] ======= Memory map: ======== 00400000-00421000 r-xp 00000000 08:41 2139283 /home/yu/app/CSA2.6/bin/wtdbg2.2/wtdbg-cns 00620000-00621000 r--p 00020000 08:41 2139283 /home/yu/app/CSA2.6/bin/wtdbg2.2/wtdbg-cns 00621000-00622000 rw-p 00021000 08:41 2139283 /home/yu/app/CSA2.6/bin/wtdbg2.2/wtdbg-cns 00ca4000-00d6f000 rw-p 00000000 00:00 0 [heap] 7fb248000000-7fb248023000 rw-p 00000000 00:00 0 7fb248023000-7fb24c000000 ---p 00000000 00:00 0 7fb250000000-7fb25002c000 rw-p 00000000 00:00 0 7fb25002c000-7fb254000000 ---p 00000000 00:00 0 7fb2557fb000-7fb2557fc000 ---p 00000000 00:00 0 7fb2557fc000-7fb255ffc000 rw-p 00000000 00:00 0 7fb258000000-7fb258023000 rw-p 00000000 00:00 0 7fb258023000-7fb25c000000 ---p 00000000 00:00 0 7fb25d878000-7fb25dc79000 rw-p 00000000 00:00 0 7fb25deee000-7fb25df7b000 rw-p 00000000 00:00 0 7fb25df7b000-7fb25dffc000 rw-p 00000000 00:00 0 7fb25dffc000-7fb25dffd000 ---p 00000000 00:00 0 7fb25dffd000-7fb25e7fd000 rw-p 00000000 00:00 0 7fb25e7fd000-7fb25e7fe000 ---p 00000000 00:00 0 7fb25e7fe000-7fb25effe000 rw-p 00000000 00:00 0 7fb25effe000-7fb25efff000 ---p 00000000 00:00 0 7fb25efff000-7fb25f7ff000 rw-p 00000000 00:00 0 7fb25f7ff000-7fb25f800000 ---p 00000000 00:00 0 7fb25f800000-7fb260000000 rw-p 00000000 00:00 0 7fb260000000-7fb260021000 rw-p 00000000 00:00 0 7fb260021000-7fb264000000 ---p 00000000 00:00 0 7fb26404a000-7fb26404b000 ---p 00000000 00:00 0 7fb26404b000-7fb26484b000 rw-p 00000000 00:00 0 7fb264d3a000-7fb264d51000 r-xp 00000000 08:41 8127216 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb264d51000-7fb264f50000 ---p 00017000 08:41 8127216 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb264f50000-7fb264f51000 r--p 00016000 08:41 8127216 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb264f51000-7fb264f52000 rw-p 00017000 08:41 8127216 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fb264f52000-7fb264f53000 ---p 00000000 00:00 0 7fb264f53000-7fb265753000 rw-p 00000000 00:00 0 7fb265753000-7fb265913000 r-xp 00000000 08:41 8133143 /lib/x86_64-linux-gnu/libc-2.23.so 7fb265913000-7fb265b13000 ---p 001c0000 08:41 8133143 /lib/x86_64-linux-gnu/libc-2.23.so 7fb265b13000-7fb265b17000 r--p 001c0000 08:41 8133143 /lib/x86_64-linux-gnu/libc-2.23.so 7fb265b17000-7fb265b19000 rw-p 001c4000 08:41 8133143 /lib/x86_64-linux-gnu/libc-2.23.so 7fb265b19000-7fb265b1d000 rw-p 00000000 00:00 0 7fb265b1d000-7fb265b36000 r-xp 00000000 08:41 8126974 /lib/x86_64-linux-gnu/libz.so.1.2.8 7fb265b36000-7fb265d35000 ---p 00019000 08:41 8126974 /lib/x86_64-linux-gnu/libz.so.1.2.8 7fb265d35000-7fb265d36000 r--p 00018000 08:41 8126974 /lib/x86_64-linux-gnu/libz.so.1.2.8 7fb265d36000-7fb265d37000 rw-p 00019000 08:41 8126974 /lib/x86_64-linux-gnu/libz.so.1.2.8 7fb265d37000-7fb265d4f000 r-xp 00000000 08:41 8133127 /lib/x86_64-linux-gnu/libpthread-2.23.so 7fb265d4f000-7fb265f4e000 ---p 00018000 08:41 8133127 /lib/x86_64-linux-gnu/libpthread-2.23.so 7fb265f4e000-7fb265f4f000 r--p 00017000 08:41 8133127 /lib/x86_64-linux-gnu/libpthread-2.23.so 7fb265f4f000-7fb265f50000 rw-p 00018000 08:41 8133127 /lib/x86_64-linux-gnu/libpthread-2.23.so 7fb265f50000-7fb265f54000 rw-p 00000000 00:00 0 7fb265f54000-7fb265f5b000 r-xp 00000000 08:41 8130839 /lib/x86_64-linux-gnu/librt-2.23.so 7fb265f5b000-7fb26615a000 ---p 00007000 08:41 8130839 /lib/x86_64-linux-gnu/librt-2.23.so 7fb26615a000-7fb26615b000 r--p 00006000 08:41 8130839 /lib/x86_64-linux-gnu/librt-2.23.so 7fb26615b000-7fb26615c000 rw-p 00007000 08:41 8130839 /lib/x86_64-linux-gnu/librt-2.23.so 7fb26615c000-7fb266264000 r-xp 00000000 08:41 8133146 /lib/x86_64-linux-gnu/libm-2.23.so 7fb266264000-7fb266463000 ---p 00108000 08:41 8133146 /lib/x86_64-linux-gnu/libm-2.23.so 7fb266463000-7fb266464000 r--p 00107000 08:41 8133146 /lib/x86_64-linux-gnu/libm-2.23.so 7fb266464000-7fb266465000 rw-p 00108000 08:41 8133146 /lib/x86_64-linux-gnu/libm-2.23.so 7fb266465000-7fb26648b000 r-xp 00000000 08:41 8133125 /lib/x86_64-linux-gnu/ld-2.23.so 7fb2664b8000-7fb2664dc000 rw-p 00000000 00:00 0 7fb2664fd000-7fb26653e000 rw-p 00000000 00:00 0 7fb26663f000-7fb266665000 rw-p 00000000 00:00 0 7fb266668000-7fb26668a000 rw-p 00000000 00:00 0 7fb26668a000-7fb26668b000 r--p 00025000 08:41 8133125 /lib/x86_64-linux-gnu/ld-2.23.so 7fb26668b000-7fb26668c000 rw-p 00026000 08:41 8133125 /lib/x86_64-linux-gnu/ld-2.23.so 7fb26668c000-7fb26668d000 rw-p 00000000 00:00 0 7ffe3c556000-7ffe3c578000 rw-p 00000000 00:00 0 [stack] 7ffe3c5c3000-7ffe3c5c5000 r--p 00000000 00:00 0 [vvar] 7ffe3c5c5000-7ffe3c5c7000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Error in `/home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns': free(): corrupted unsorted chunks: 0x00000000010c7da0 ====== Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f4be27617e5] /lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f4be276a37a] /lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f4be276e53c] /home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns[0x404415] /home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns[0x4036e1] /lib/x86_64-linux-gnu/libpthread.so.0(+0x76ba)[0x7f4be2cd56ba] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f4be27f141d] ======= Memory map: ======== 00400000-00421000 r-xp 00000000 08:41 2139283 /home/yu/app/CSA2.6/bin/wtdbg2.2/wtdbg-cns 00620000-00621000 r--p 00020000 08:41 2139283 /home/yu/app/CSA2.6/bin/wtdbg2.2/wtdbg-cns 00621000-00622000 rw-p 00021000 08:41 2139283 /home/yu/app/CSA2.6/bin/wtdbg2.2/wtdbg-cns 010c7000-01175000 rw-p 00000000 00:00 0 [heap] 7f4bcc000000-7f4bcc023000 rw-p 00000000 00:00 0 7f4bcc023000-7f4bd0000000 ---p 00000000 00:00 0 7f4bd0000000-7f4bd002c000 rw-p 00000000 00:00 0 7f4bd002c000-7f4bd4000000 ---p 00000000 00:00 0 7f4bd4000000-7f4bd4023000 rw-p 00000000 00:00 0 7f4bd4023000-7f4bd8000000 ---p 00000000 00:00 0 7f4bd9ffc000-7f4bd9ffd000 ---p 00000000 00:00 0 7f4bd9ffd000-7f4bda7fd000 rw-p 00000000 00:00 0 7f4bda7fd000-7f4bda7fe000 ---p 00000000 00:00 0 7f4bda7fe000-7f4bdaffe000 rw-p 00000000 00:00 0 7f4bdaffe000-7f4bdafff000 ---p 00000000 00:00 0 7f4bdafff000-7f4bdb7ff000 rw-p 00000000 00:00 0 7f4bdb7ff000-7f4bdb800000 ---p 00000000 00:00 0 7f4bdb800000-7f4bdc000000 rw-p 00000000 00:00 0 7f4bdc000000-7f4bdc021000 rw-p 00000000 00:00 0 7f4bdc021000-7f4be0000000 ---p 00000000 00:00 0 7f4be0416000-7f4be0617000 rw-p 00000000 00:00 0 7f4be0617000-7f4be06a4000 rw-p 00000000 00:00 0 7f4be071e000-7f4be075f000 rw-p 00000000 00:00 0 7f4be075f000-7f4be07e0000 rw-p 00000000 00:00 0 7f4be07e0000-7f4be07e1000 ---p 00000000 00:00 0 7f4be07e1000-7f4be0fe1000 rw-p 00000000 00:00 0 7f4be0fe1000-7f4be0fe2000 ---p 00000000 00:00 0 7f4be0fe2000-7f4be17e2000 rw-p 00000000 00:00 0 7f4be1cd1000-7f4be1ce8000 r-xp 00000000 08:41 8127216 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f4be1ce8000-7f4be1ee7000 ---p 00017000 08:41 8127216 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f4be1ee7000-7f4be1ee8000 r--p 00016000 08:41 8127216 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f4be1ee8000-7f4be1ee9000 rw-p 00017000 08:41 8127216 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f4be1ee9000-7f4be1eea000 ---p 00000000 00:00 0 7f4be1eea000-7f4be26ea000 rw-p 00000000 00:00 0 7f4be26ea000-7f4be28aa000 r-xp 00000000 08:41 8133143 /lib/x86_64-linux-gnu/libc-2.23.so 7f4be28aa000-7f4be2aaa000 ---p 001c0000 08:41 8133143 /lib/x86_64-linux-gnu/libc-2.23.so 7f4be2aaa000-7f4be2aae000 r--p 001c0000 08:41 8133143 /lib/x86_64-linux-gnu/libc-2.23.so 7f4be2aae000-7f4be2ab0000 rw-p 001c4000 08:41 8133143 /lib/x86_64-linux-gnu/libc-2.23.so 7f4be2ab0000-7f4be2ab4000 rw-p 00000000 00:00 0 7f4be2ab4000-7f4be2acd000 r-xp 00000000 08:41 8126974 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f4be2acd000-7f4be2ccc000 ---p 00019000 08:41 8126974 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f4be2ccc000-7f4be2ccd000 r--p 00018000 08:41 8126974 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f4be2ccd000-7f4be2cce000 rw-p 00019000 08:41 8126974 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f4be2cce000-7f4be2ce6000 r-xp 00000000 08:41 8133127 /lib/x86_64-linux-gnu/libpthread-2.23.so 7f4be2ce6000-7f4be2ee5000 ---p 00018000 08:41 8133127 /lib/x86_64-linux-gnu/libpthread-2.23.so 7f4be2ee5000-7f4be2ee6000 r--p 00017000 08:41 8133127 /lib/x86_64-linux-gnu/libpthread-2.23.so 7f4be2ee6000-7f4be2ee7000 rw-p 00018000 08:41 8133127 /lib/x86_64-linux-gnu/libpthread-2.23.so 7f4be2ee7000-7f4be2eeb000 rw-p 00000000 00:00 0 7f4be2eeb000-7f4be2ef2000 r-xp 00000000 08:41 8130839 /lib/x86_64-linux-gnu/librt-2.23.so 7f4be2ef2000-7f4be30f1000 ---p 00007000 08:41 8130839 /lib/x86_64-linux-gnu/librt-2.23.so 7f4be30f1000-7f4be30f2000 r--p 00006000 08:41 8130839 /lib/x86_64-linux-gnu/librt-2.23.so 7f4be30f2000-7f4be30f3000 rw-p 00007000 08:41 8130839 /lib/x86_64-linux-gnu/librt-2.23.so 7f4be30f3000-7f4be31fb000 r-xp 00000000 08:41 8133146 /lib/x86_64-linux-gnu/libm-2.23.so 7f4be31fb000-7f4be33fa000 ---p 00108000 08:41 8133146 /lib/x86_64-linux-gnu/libm-2.23.so 7f4be33fa000-7f4be33fb000 r--p 00107000 08:41 8133146 /lib/x86_64-linux-gnu/libm-2.23.so 7f4be33fb000-7f4be33fc000 rw-p 00108000 08:41 8133146 /lib/x86_64-linux-gnu/libm-2.23.so 7f4be33fc000-7f4be3422000 r-xp 00000000 08:41 8133125 /lib/x86_64-linux-gnu/ld-2.23.so 7f4be344f000-7f4be3473000 rw-p 00000000 00:00 0 7f4be34a4000-7f4be34d5000 rw-p 00000000 00:00 0 7f4be35d6000-7f4be35fc000 rw-p 00000000 00:00 0 7f4be35ff000-7f4be3621000 rw-p 00000000 00:00 0 7f4be3621000-7f4be3622000 r--p 00025000 08:41 8133125 /lib/x86_64-linux-gnu/ld-2.23.so 7f4be3622000-7f4be3623000 rw-p 00026000 08:41 8133125 /lib/x86_64-linux-gnu/ld-2.23.so 7f4be3623000-7f4be3624000 rw-p 00000000 00:00 0 7ffce54ce000-7ffce54f0000 rw-p 00000000 00:00 0 [stack] 7ffce55d1000-7ffce55d3000 r--p 00000000 00:00 0 [vvar] 7ffce55d3000-7ffce55d5000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] ** Error in /home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns': free(): corrupted unsorted chunks: 0x00000000025beda0 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fab1f8af7e5] /lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7fab1f8b837a] /lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7fab1f8bc53c] /home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns[0x404415] /home/yu/app/CSA2.6/INSTALL/../bin/wtdbg2.2/wtdbg-cns[0x4036e1] /lib/x86_64-linux-gnu/libpthread.so.0(+0x76ba)[0x7fab1fe236ba] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7fab1f93f41d] ======= Memory map: ======== 00400000-00421000 r-xp 00000000 08:41 2139283 /home/yu/app/CSA2.6/bin/wtdbg2.2/wtdbg-cns 00620000-00621000 r--p 00020000 08:41 2139283 /home/yu/app/CSA2.6/bin/wtdbg2.2/wtdbg-cns 00621000-00622000 rw-p 00021000 08:41 2139283 /home/yu/app/CSA2.6/bin/wtdbg2.2/wtdbg-cns 025be000-0268d000 rw-p 00000000 00:00 0 [heap] 7fab08000000-7fab08023000 rw-p 00000000 00:00 0 7fab08023000-7fab0c000000 ---p 00000000 00:00 0 7fab0f4fd000-7fab0f6fe000 rw-p 00000000 00:00 0 7fab0f7ff000-7fab0f800000 ---p 00000000 00:00 0 7fab0f800000-7fab10000000 rw-p 00000000 00:00 0 7fab10000000-7fab10023000 rw-p 00000000 00:00 0 7fab10023000-7fab14000000 ---p 00000000 00:00 0 7fab14000000-7fab14023000 rw-p 00000000 00:00 0 7fab14023000-7fab18000000 ---p 00000000 00:00 0 7fab18000000-7fab18021000 rw-p 00000000 00:00 0 7fab18021000-7fab1c000000 ---p 00000000 00:00 0 7fab1c029000-7fab1c0aa000 rw-p 00000000 00:00 0 7fab1c0e4000-7fab1c12b000 rw-p 00000000 00:00 0 7fab1c12b000-7fab1c12c000 ---p 00000000 00:00 0 7fab1c12c000-7fab1c92c000 rw-p 00000000 00:00 0 7fab1c92c000-7fab1c92d000 ---p 00000000 00:00 0 7fab1c92d000-7fab1d12d000 rw-p 00000000 00:00 0 7fab1d12d000-7fab1d12e000 ---p 00000000 00:00 0 7fab1d12e000-7fab1d92e000 rw-p 00000000 00:00 0 7fab1d92e000-7fab1d92f000 ---p 00000000 00:00 0 7fab1d92f000-7fab1e12f000 rw-p 00000000 00:00 0 7fab1e12f000-7fab1e130000 ---p 00000000 00:00 0 7fab1e130000-7fab1e930000 rw-p 00000000 00:00 0 7fab1ee1f000-7fab1ee36000 r-xp 00000000 08:41 8127216 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fab1ee36000-7fab1f035000 ---p 00017000 08:41 8127216 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fab1f035000-7fab1f036000 r--p 00016000 08:41 8127216 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fab1f036000-7fab1f037000 rw-p 00017000 08:41 8127216 /lib/x86_64-linux-gnu/libgcc_s.so.1 7fab1f037000-7fab1f038000 ---p 00000000 00:00 0 7fab1f038000-7fab1f838000 rw-p 00000000 00:00 0 7fab1f838000-7fab1f9f8000 r-xp 00000000 08:41 8133143 /lib/x86_64-linux-gnu/libc-2.23.so 7fab1f9f8000-7fab1fbf8000 ---p 001c0000 08:41 8133143 /lib/x86_64-linux-gnu/libc-2.23.so 7fab1fbf8000-7fab1fbfc000 r--p 001c0000 08:41 8133143 /lib/x86_64-linux-gnu/libc-2.23.so 7fab1fbfc000-7fab1fbfe000 rw-p 001c4000 08:41 8133143 /lib/x86_64-linux-gnu/libc-2.23.so 7fab1fbfe000-7fab1fc02000 rw-p 00000000 00:00 0 7fab1fc02000-7fab1fc1b000 r-xp 00000000 08:41 8126974 /lib/x86_64-linux-gnu/libz.so.1.2.8 7fab1fc1b000-7fab1fe1a000 ---p 00019000 08:41 8126974 /lib/x86_64-linux-gnu/libz.so.1.2.8 7fab1fe1a000-7fab1fe1b000 r--p 00018000 08:41 8126974 /lib/x86_64-linux-gnu/libz.so.1.2.8 7fab1fe1b000-7fab1fe1c000 rw-p 00019000 08:41 8126974 /lib/x86_64-linux-gnu/libz.so.1.2.8 7fab1fe1c000-7fab1fe34000 r-xp 00000000 08:41 8133127 /lib/x86_64-linux-gnu/libpthread-2.23.so 7fab1fe34000-7fab20033000 ---p 00018000 08:41 8133127 /lib/x86_64-linux-gnu/libpthread-2.23.so 7fab20033000-7fab20034000 r--p 00017000 08:41 8133127 /lib/x86_64-linux-gnu/libpthread-2.23.so 7fab20034000-7fab20035000 rw-p 00018000 08:41 8133127 /lib/x86_64-linux-gnu/libpthread-2.23.so 7fab20035000-7fab20039000 rw-p 00000000 00:00 0 7fab20039000-7fab20040000 r-xp 00000000 08:41 8130839 /lib/x86_64-linux-gnu/librt-2.23.so 7fab20040000-7fab2023f000 ---p 00007000 08:41 8130839 /lib/x86_64-linux-gnu/librt-2.23.so 7fab2023f000-7fab20240000 r--p 00006000 08:41 8130839 /lib/x86_64-linux-gnu/librt-2.23.so 7fab20240000-7fab20241000 rw-p 00007000 08:41 8130839 /lib/x86_64-linux-gnu/librt-2.23.so 7fab20241000-7fab20349000 r-xp 00000000 08:41 8133146 /lib/x86_64-linux-gnu/libm-2.23.so 7fab20349000-7fab20548000 ---p 00108000 08:41 8133146 /lib/x86_64-linux-gnu/libm-2.23.so 7fab20548000-7fab20549000 r--p 00107000 08:41 8133146 /lib/x86_64-linux-gnu/libm-2.23.so 7fab20549000-7fab2054a000 rw-p 00108000 08:41 8133146 /lib/x86_64-linux-gnu/libm-2.23.so 7fab2054a000-7fab20570000 r-xp 00000000 08:41 8133125 /lib/x86_64-linux-gnu/ld-2.23.so 7fab2059d000-7fab205c1000 rw-p 00000000 00:00 0 7fab205c1000-7fab20602000 rw-p 00000000 00:00 0 7fab20724000-7fab2074a000 rw-p 00000000 00:00 0 7fab2074d000-7fab2076f000 rw-p 00000000 00:00 0 7fab2076f000-7fab20770000 r--p 00025000 08:41 8133125 /lib/x86_64-linux-gnu/ld-2.23.so 7fab20770000-7fab20771000 rw-p 00026000 08:41 8133125 /lib/x86_64-linux-gnu/ld-2.23.so 7fab20771000-7fab20772000 rw-p 00000000 00:00 0 7ffc869d6000-7ffc869f8000 rw-p 00000000 00:00 0 [stack] 7ffc869fc000-7ffc869fe000 r--p 00000000 00:00 0 [vvar] 7ffc869fe000-7ffc86a00000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] It is frustrated that I can't find the server with higher RAM.

[HMPNK]

At least the first two steps look promising. The steps in 03 and 04 typically need less memory.

Try this:

remove "set -e" remove "set -o pipefail" from STEP_03.bash

and rerun this script in directory 03_... (nohup bash STEP_03.bash) , this should run all commands, even if errors occur.

If that works you can go back to your CSA-Pipeline script (cd ../..; EDIT script/CAS.sh) and run only the last steps regarding STEP4 (include the export commands at the beginning of the script; cd xxx, mkdir xxx, STEP_04.bash).

[HMPNK]

It would also be interesting what Linux distribution your server runs.

[HMPNK]

I just found a bug that occurs if the list of reassembly jobs is very long (>13253 on our system, depends on xargs).

Could you check the number of lines of this file *wtdbg-BATCH-ALL-RUNS.sh in folder 03 ? Could you also check if "total" occurs in that file? If yes, the crash in STEP03 is related to this.

I have updated the code, please reinstall CSA from github and try again.

[ch8316f5eyu]

Thank you for your prompt reply. The linux distribution: Linux version 4.4.0-184-generic (buildd@lgw01-amd64-060) (gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.12) ) #214-Ubuntu SMP Thu Jun 4 10:14:11 UTC 2020 But there is still error when I run the step 4, there is all the output message of step4: ` Sun Jun 21 04:32:26 CST 2020 RUN WHOLE GENOME ALIGNMENT BY LAST

Sun Jun 21 06:32:12 CST 2020 RUN RAGOUT TO ORDER CONTIGS ACCORDING TO REFERENCE There is the content of ragout.log: [06:32:12] INFO: Cooking Ragout... [06:32:12] INFO: Reading FASTA with contigs [06:33:44] INFO: Converting MAF to synteny Usage: maf2synteny [-o out_dir] [-s simpl_params] [-m block_sizes] maf_file

positional arguments:

-------maf_file>-------path to maf file

optional arguments:

--------o out_dir>-----path to the output directory [default = .] --------s simpl_params>path to a file with custom simplification parameters [default = not set] --------b block_sizes>-comma-separated list of synteny block scales [default = 5000] [06:33:44] ERROR: Some error inside native ragout-maf2synteny module [06:33:44] ERROR: Something went wrong with maf2synteny [06:33:44] ERROR: There were problems with synteny backend, exiting. `

[ch8316f5eyu]

The number of lines of N33.step2.fa.wtdbg-BATCH-ALL-RUNS.sh is 7223. The step3 succeeded when I deleted the two line code according to what you said.

[HMPNK]

The error in RAGOUT is due to the environment variables not set. Before running STEP_04.bash, you will need to set:

export PATH="your path"/CSA2.6/INSTALL/../bin/RAGOUT_V1.0/lib:$PATH export PYTHONPATH="your path"/CSA2.6/INSTALL/../bin/RAGOUT_V1.0/lib

You have to replace "your path", by the path where you installed CSA.

Could you please post the Contig statistics after step_03?

[ch8316f5eyu]

STEP3 GAP CLOSED CONTIG STATS: Total: 2443778488 Count: 3944 Average: 619619.29 Median: 53101 N00: 28648872 1 N10: 10834336 17 N20: 8016401 42 N30: 6651974 75 N40: 5104462 118 N50: 4126746 170 N60: 3095737 239 N70: 2227178 331 N80: 1329461 473 N90: 521975 751 N100: 5002 3944

[HMPNK]

Looks good, the gap reassembly worked and improved Contig N50 3.2-fold! I guess your using a relatively low coverage dataset 10-20X and this is why you can run the assembly on only 188G RAM.

[ch8316f5eyu]

Thank you for your help! CSA succeeded!

[HMPNK]

Great! Thanks for your feedback, it helped to improve the pipeline. Would you share the final contig and scaffold statistics?

[ch8316f5eyu]

FINAL CONTIG STATS: Total: 2443172620 Count: 3745 Average: 652382.54 Median: 51018 N00: 28648872 1 N10: 12126993 16 N20: 9488405 38 N30: 7049521 69 N40: 5656134 108 N50: 4723955 155 N60: 3579919 215 N70: 2599312 294 N80: 1489703 417 N90: 590722 664 N100: 5002 3745

FINAL SCAFFOLD STATS: Total: 2492961929 Count: 1339 Average: 1861808.76 Median: 15090 N00: 187901165 1 N10: 173405562 2 N20: 165873924 3 N30: 145636299 5 N40: 140845982 7 N50: 124829477 9 N60: 118960978 11 N70: 111433577 13 N80: 106029421 15 N90: 88410764 18 N100: 5002 1339