Script base path does not exist or is not a directory: /home/ubuntu/bin

[monagai]

I'm running Nanoseq 3.5.0 using nextflow in a Docker container. I arranged a Dockerfile here because it does not include Java and nextflow. I don't use module and sigularity. I use fastq as input.

My Nanoseq fails. In .nextflow.log, I found the error message Script base path does not exist or is not a directory: /home/ubuntu/bin.

What is the "script base path"? What should be placed under /home/ubuntu/bin? nextflow? Nanoseq scripts?

[detail]

....
Oct-18 08:03:19.091 [main] DEBUG nextflow.Session - Session UUID: 90cba058-7e70-4103-9731-6803b81e2238
Oct-18 08:03:19.091 [main] DEBUG nextflow.Session - Run name: voluminous_knuth
Oct-18 08:03:19.092 [main] DEBUG nextflow.Session - Executor pool size: 32
Oct-18 08:03:19.103 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Oct-18 08:03:19.111 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Oct-18 08:03:19.161 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 23.10.0 build 5889
  Created: 15-10-2023 15:07 UTC 
  System: Linux 3.10.0-1160.53.1.el7.x86_64
  Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 11.0.20.1+1-post-Ubuntu-0ubuntu122.04
  Encoding: UTF-8 (UTF-8)
  Process: 1@937c69528046 [172.17.0.2]
  CPUs: 32 - Mem: 251.9 GB (123 GB) - Swap: 32 GB (22.2 GB)
Oct-18 08:03:19.203 [main] DEBUG nextflow.Session - Work-dir: /home/ubuntu/work [xfs]
Oct-18 08:03:19.204 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/ubuntu/bin
Oct-18 08:03:19.219 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-18 08:03:19.236 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-18 08:03:19.277 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Oct-18 08:03:19.320 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 33; maxThreads: 1000
Oct-18 08:03:19.434 [main] DEBUG nextflow.Session - Session start
Oct-18 08:03:22.578 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-18 08:03:22.643 [main] INFO  nextflow.script.BaseScript - /home/ubuntu/info.csv
Oct-18 08:03:22.832 [main] INFO  nextflow.script.BaseScript - 
...

• /home/ubuntu/info.csv: sample sheet csv I prepared for Nanoseq.

I have read the following issue. https://github.com/cancerit/NanoSeq/issues/42 It seems there is no answer.

[fa8sanger]

Hi, I am afraid the Nextflow script is not mature enough yet. I'd advise to run the pipeline directly with runNanoSeq.py. Not sure why #42 was closed without a reply, that's strange

[monagai]

I really thank you for your quick reply. I will execute Nanoseq step by step following your advice.

[fa8sanger]

Good! Let me know if you encounter any problem and I’ll be happy to help

On 18 Oct 2023, at 12:39, Momoko NAGAI @.***> wrote:

I really thank you for your quick reply. I will execute Nanoseq step by step following your advice.

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