LiftOver chain files for new version tree shrew genome and rabbit genome to human genome conversions

Lin Ou

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Sep 12, 2025, 2:05:05 PMSep 12

to UCSC Genome Browser Public Support

Dear UCSC staff:

I'm a Ph.D candidate from Tsinghua University, and recently I'm trying to map genomic coordinates from the tree shrew genome(TS_3.0 genome annotation, http://www.treeshrewdb.org/download.html) to human genome(hg38) and from rabbit genome(Genome assembly OryCun3.0, https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_013371645.1/) to human genome(hg38).

First I used your program LiftOver (thank you for making it available for so many species!), however the available version of tree shrew genome and rabbit genome are not what I am using now. Hence, I'm attempting to build the necessary chain files following the directions provided here :
http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl.

But then I faced the “timed out” problem. Even though I tried to install the Parasol job control system following the procedure and succeed:

http://genomewiki.ucsc.edu/index.php/Parasol_job_control_system

when I got back to build chain file, the problem still existed, like this:

29052 jobs in batch

0 jobs (including everybody's) in Parasol queue or running.

Checking finished jobs

updated job database on disk

Pushed Jobs: 29052

================

Checking job status 0 minutes after launch

29052 jobs in batch

0 jobs (including everybody's) in Parasol queue or running.

Sick Batch: consecutive crashes (45) >= sick batch threshold (25)

Checking finished jobs

updated job database on disk

total sick machines: 1 failures: 45

Sick batch! will sleep 10 minutes, clear sick nodes and retry

rudpSend timed out

pmSendString timed out!

pmSendString: will sleep 60 seconds and retry

Told hub to clear sick nodes

================

Checking job status 11 minutes after launch

29052 jobs in batch

0 jobs (including everybody's) in Parasol queue or running.

Checking finished jobs

updated job database on disk

Pushed Jobs: 29052

Retried jobs: 29052

Have you encountered this problem before, and do you know how to solve this problem? perhaps there might be an update or some other documentation for chain-file generation besides the link above? If possible, would you please provide us the new version chain files?

I have tried to make this chain files for several weeks and I feel sorry because your team already provided detailed guidance. Besides, I was running these procedures in a single pod built from a cluster, and I don’t know if my configuration is suitable for this task. Any more suggestions from you would be very helpful.

Thanks very much again for providing this valuable resource for the community. Wish you better and better!

best regards,

Lin Ou

Luis Nassar

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Sep 15, 2025, 6:15:54 PMSep 15

to Lin Ou, UCSC Genome Browser Public Support

Hello, Lin.

That documentation is the best we have; it's a technical pipeline originally designed for our system, so it is not uncommon for issues to come up when others run it.

We can generate the chain files you are looking for, GCA_013371645.1 to hg38 is not a problem, but we do require that the genome have an NCBI accession, e.g., GCA or GCF. Is TS_3.0 not in NCBI Genbank?

We see version 2 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_033439345.1/), but that may not be suitable for you, let us know.

If you would like to try and debug the chain pipeline, one of our engineers shares the following:

This means that communication from node process to hub process is failing with a timeout,
so it is not connecting. This could be because the paraHub daemon is not running.
Or perhaps a firewall interferes, although that is much less common on internal
machines that are not acting as web servers so they do not need as much security.
What shell is the user running commands in.
Internally we use bash shell, I suggest the user might run it in their bash shell too.

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Lou Nassar
UCSC Genomics Institute

Lin Ou

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Sep 19, 2025, 2:20:59 PMSep 19

to UCSC Genome Browser Public Support, Luis Nassar, UCSC Genome Browser Public Support

Hello, Luis.

Thank you so much for your quick reply and help! You’re so kind for helping me build the chain files and deal with the bugs!

For the new tree shrew version you mentioned

( https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_033439345.1/), it is suitable for us, the sequence are the same, but there is a little difference in the chromosome name, like this, the partial content in red box is from NCBI, and the content in green box is from ours:

For the chain pipeline, I also run it in our bash shell. So, the problem maybe the firewall interferes, which I don’t have the authority to check and change (so pity!).

But recently, when I browsed and traced back the mailing lists of similar problems (thanks again for dealing with our mails patiently and timely!), I found an alternative method by using nf-lo(https://nf-lo.readthedocs.io/en/latest/index.html):

Then I tried according to the tutorial, and successfully generated many single chains. However, the run failed at “chainMergeSort: Argument list too long”. The end of the content in the “.nextflow.log” file is shown below:

Sep-18 15:37:41.695 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for

task: name=LASTZ:chainMerge (chainmerge); work-dir=/home/oulin/software/chain_files/treeshrewTohuman4/work/b8/4cfd7ca26cfc3b83fdb6cee431f86b

error [nextflow.exception.ProcessFailedException]: Process `LASTZ:chainMerge (chainmerge)` terminated with an error exit status (1)

Sep-18 15:37:41.695 [TaskFinalizer-5] INFO nextflow.processor.TaskProcessor - [b8/4cfd7c] NOTE: Process `LASTZ:chainMerge (chainmerge)` terminated with an error exit status (1) -- Error is ignored

Sep-18 15:37:41.697 [main] DEBUG nextflow.Session - Session await > all processes finished

Sep-18 15:37:41.793 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop

Sep-18 15:37:41.793 [main] DEBUG nextflow.Session - Session await > all barriers passed

Sep-18 15:37:41.808 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)

Sep-18 15:37:41.809 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)

Sep-18 15:37:41.915 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1074826; failedCount=3; ignoredCount=1; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=2; abortedCount=0; succeedDuration=1d 14h 4m 59s; failedDuration=1h 10m; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=52; peakCpus=52; peakMemory=263 GB; ]

Sep-18 15:37:41.915 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file

Sep-18 15:37:41.934 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report

Sep-18 15:39:25.197 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline

Sep-18 15:39:37.400 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done

Sep-18 15:39:37.521 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)

Sep-18 15:39:37.521 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

It really upset me very much. Have you encountered this problem? Any more advice will be helpful, and I will do my best to try.

Thanks very much again! You are really nice! Wish you better and better!

I may bother you too much (so sorry! I will try my best to create chains myself), but it will be even helpful for us if these chain files can be also available:

human(hg38) to tree shrew (TS_3.0),

human(hg38) to rabbit (OryCun3.0),

tree shrew (TS_3.0) to mouse(mm10),

rabbit (OryCun3.0) to mouse(mm10),

mouse(mm10) to tree shrew (TS_3.0) and

mouse(mm10) to rabbit (OryCun3.0).

best regards,

Lin Ou

Luis Nassar

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Sep 22, 2025, 6:25:43 PMSep 22

to Lin Ou, UCSC Genome Browser Public Support

Hi, Lin.

We started generating those liftOver files; they should be ready this week or next week at the latest.

If that is OK, then we can stop trying to troubleshoot the pipeline.

On Thu, Sep 18, 2025 at 10:27 PM Lin Ou <ouli...@gmail.com> wrote:

Hello, Luis.

Thank you so much for your quick reply and help! You’re so kind for helping me build the chain files and deal with the bugs!

For the new tree shrew version you mentioned

( https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_033439345.1/), it is the same genome version we are using, but there is a little difference in the chromosome name, like this, the partial content in red box is from NCBI, and the content in green box is from ours, could you please change the chromosome for us if possible:

For the chain pipeline, I also run it in our bash shell. So, the problem maybe the firewall interferes, which I don’t have the authority to check and change (so pity!).

But recently, when I browsed and traced back the mailing lists of similar problems (thanks again for dealing with our mails patiently and timely!), I found an alternative method by using nf-lo(https://nf-lo.readthedocs.io/en/latest/index.html).

Then I tried according to the tutorial, and successfully generated many single chains. However, the run failed at “chainMergeSort: Argument list too long”. The end of the content in the “.nextflow.log” file is shown below:

Sep-18 15:37:41.695 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for

task: name=LASTZ:chainMerge (chainmerge); work-dir=/home/oulin/software/chain_files/treeshrewTohuman4/work/b8/4cfd7ca26cfc3b83fdb6cee431f86b

error [nextflow.exception.ProcessFailedException]: Process `LASTZ:chainMerge (chainmerge)` terminated with an error exit status (1)

Sep-18 15:37:41.695 [TaskFinalizer-5] INFO nextflow.processor.TaskProcessor - [b8/4cfd7c] NOTE: Process `LASTZ:chainMerge (chainmerge)` terminated with an error exit status (1) -- Error is ignored

Sep-18 15:37:41.697 [main] DEBUG nextflow.Session - Session await > all processes finished

Sep-18 15:37:41.793 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop

Sep-18 15:37:41.793 [main] DEBUG nextflow.Session - Session await > all barriers passed

Sep-18 15:37:41.808 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)

Sep-18 15:37:41.809 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)

Sep-18 15:37:41.915 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1074826; failedCount=3; ignoredCount=1; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=2; abortedCount=0; succeedDuration=1d 14h 4m 59s; failedDuration=1h 10m; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=52; peakCpus=52; peakMemory=263 GB; ]

Sep-18 15:37:41.915 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file

Sep-18 15:37:41.934 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report

Sep-18 15:39:25.197 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline

Sep-18 15:39:37.400 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done

Sep-18 15:39:37.521 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)

Sep-18 15:39:37.521 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

It really upset me very much. Have you encountered this problem? Any more advice will be helpful, and I will do my best to try.

Thanks very much again! You are really nice! Wish you better and better!

I may bother you too much (so sorry! I will try my best to create chains myself), but it will be even helpful for us if these chain files can be also available:

human(hg38) to tree shrew (Genome assembly KIZ version 2),

human(hg38) to rabbit (OryCun3.0),

tree shrew (Genome assembly KIZ version 2) to mouse(mm10),

rabbit (OryCun3.0) to mouse(mm10),

mouse(mm10) to tree shrew (Genome assembly KIZ version 2) and

mouse(mm10) to rabbit (OryCun3.0).

The rabbit genome(OryCun3.0):

https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_013371645.1/

The tree shrew genome(Genome assembly KIZ version 2):

https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_033439345.1/

best regards,

Lin Ou

在2025年9月16日星期二 UTC+8 06:15:54<Luis Nassar> 写道：

Lin Ou

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Sep 23, 2025, 2:26:11 PMSep 23

to UCSC Genome Browser Public Support, Luis Nassar, UCSC Genome Browser Public Support

Hello, Luis.

Thanks so much! That would be great!

best regards,

Lin Ou

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Oct 8, 2025, 12:24:20 PM (2 days ago) Oct 8

to UCSC Genome Browser Public Support, Luis Nassar, UCSC Genome Browser Public Support

Hello Luis,

Sorry for bothering you!

Since you said before the chain-building process should need at most two weeks, but I still can't find renewed chain files on the website so far. So sorry, please let me know how to access these files if available. Or is there something troublesome in the building process?

Thank you again for your kindness and patience!

Best wishes,

Lin Ou

Luis Nassar

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Oct 8, 2025, 7:20:17 PM (2 days ago) Oct 8

to Lin Ou, UCSC Genome Browser Public Support

Hi, Lin.

You will find links to the files below:

Can you verify that this includes all of the files you needed?

Lin Ou

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Oct 9, 2025, 12:08:23 PM (22 hours ago) Oct 9

to UCSC Genome Browser Public Support, Luis Nassar, UCSC Genome Browser Public Support

Hi, Luis,

Thank you so much!

And there still lacks two chain files (which sorry I make mistakes in the previous email):

rabbit(GCA_013371645.1) to mouse(mm10) and

mouse(mm10) to rabbit(GCA_013371645.1).

Thanks again!

Best regards,

Lin Ou

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