Hello hifiasm developers and users,
I have run hifiasm three times, but the process was interrupted and terminated each time before generating the final GFA output files. However, there is no obvious error message in the log files.
My data and computing resources are as follows:
HiFi reads: ~160 GB
ONT ultra-long reads: ~240 GB
RAM: 2 TB
Storage: 80 TB available
CPU: 128 cores
The command I used was:
hifiasm -o 5.asm -t 64
--telo-m TTAGGG
--dual-scaf
--ul ../6.pass.ul.fastq.gz
../5_HIFI_merged.fastq.gz
The log shows that the UL index was successfully generated:
[M::uidx_l_build] Index has been built.
[M::uidx_write] Index has been written.
However, the program stops afterward, and no final GFA files (such as 5.asm.bp.p_ctg.gfa) are generated. Only intermediate files (*.bin) remain.
I have sufficient computational resources, so I am wondering whether this issue could be related to the --telo-m parameter or the telomere detection step.
Has anyone encountered a similar situation? Any suggestions on how to debug this problem would be greatly appreciated.
Thank you very much for your help.
nohup hifiasm -o 5.asm -t 64 --telo-m TTAGGG --dual-scaf --ul ../6.pass.ul.fastq.gz ../5_HIFI_merged.fastq.gz 2>&1 | tee 5.asm.log
(base) root@01:~/assembly_result$ ls -lh
total 425G
-rw-rw-r-- 1 root root 91G Jul 31 06:28 5.asm.ec.bin
-rw-rw-r-- 1 root root 0 Aug 5 00:48 5.asm.log
-rw-rw-r-- 1 root root 85K Jul 31 10:46 5.asm.log
-rw-rw-r-- 1 root root 148G Jul 31 07:05 5.asm.ovlp.reverse.bin
-rw-rw-r-- 1 root root 149G Jul 31 06:47 5.asm.ovlp.source.bin
-rw-rw-r-- 1 root root 39G Jul 31 10:49 5.asm.uidx.bin
This is the log file generated during the hifiasm running process.
log-1.txt
This is the GenomeScope2 plot generated using the online GenomeScope2 tool.
Hello hifiasm developers and users,
I have run hifiasm three times, but the process was interrupted and terminated each time before generating the final GFA output files. However, there is no obvious error message in the log files.
My data and computing resources are as follows:
HiFi reads: ~160 GB
ONT ultra-long reads: ~240 GB
RAM: 2 TB
Storage: 80 TB available
CPU: 128 cores
The command I used was:
hifiasm -o 5.asm -t 64
--telo-m TTAGGG
--dual-scaf
--ul ../6.pass.ul.fastq.gz
../5_HIFI_merged.fastq.gz
The log shows that the UL index was successfully generated:
[M::uidx_l_build] Index has been built.
[M::uidx_write] Index has been written.
However, the program stops afterward, and no final GFA files (such as 5.asm.bp.p_ctg.gfa) are generated. Only intermediate files (*.bin) remain.
I have sufficient computational resources, so I am wondering whether this issue could be related to the --telo-m parameter or the telomere detection step.
Has anyone encountered a similar situation? Any suggestions on how to debug this problem would be greatly appreciated.
Thank you very much for your help.
nohup hifiasm -o 5.asm -t 64 --telo-m TTAGGG --dual-scaf --ul ../6.pass.ul.fastq.gz ../5_HIFI_merged.fastq.gz 2>&1 | tee 5.asm.log
(base) root@01:~/assembly_result$ ls -lh
total 425G
-rw-rw-r-- 1 root root 91G Jul 31 06:28 5.asm.ec.bin
-rw-rw-r-- 1 root root 0 Aug 5 00:48 5.asm.log
-rw-rw-r-- 1 root root 85K Jul 31 10:46 5.asm.log
-rw-rw-r-- 1 root root 148G Jul 31 07:05 5.asm.ovlp.reverse.bin
-rw-rw-r-- 1 root root 149G Jul 31 06:47 5.asm.ovlp.source.bin
-rw-rw-r-- 1 root root 39G Jul 31 10:49 5.asm.uidx.bin
This is the log file generated during the hifiasm running process.
log-1.txt
This is the GenomeScope2 plot generated using the online GenomeScope2 tool.