# Snakefile not found **URL:** \ **Category:** Uncategorized\ **Created:** [April 27, 2021, 8:19am UTC](https://nextstrain.discourse.group/t/snakefile-not-found/507 "2021-04-27T08:19:40Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![SophieLuiWi](https://avatars.discourse-cdn.com/v4/letter/s/c77e96/32.png) [@SophieLuiWi](https://nextstrain.discourse.group/u/SophieLuiWi)\ **Post date:** [April 27, 2021, 8:19am UTC](https://nextstrain.discourse.group/t/snakefile-not-found/507/1 "2021-04-27T08:19:40Z")
Hey, I’m trying to run the zika-tutorial from a windows computer (using cygwin) and cannot get past: Error: no Snakefile found, tried Snakefile, snakefile, workflow/Snakefile, workf low/snakefile. Has anyone had a similar problem? The Snakefile seems completely fine, I can read it and all the tutorial files were downloaded well (I tried both downloading and cloning the repository using git). Thanks a lot! ---
**Author:** ![trs](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/trs/32/5_2.png) [@trs](https://nextstrain.discourse.group/u/trs)\ **Post date:** [April 27, 2021, 4:45pm UTC](https://nextstrain.discourse.group/t/snakefile-not-found/507/2 "2021-04-27T16:45:05Z")
Hi @SophieLuiWi, welcome! This suggests to me that Snakemake ends up running in a different directory than you expect, one that isn’t the `zika-tutorial` build directory. Two things that would help troubleshoot this: 1. Can you share the exact command you’re running? It’s essential to know if you’re using the `nextstrain build` command or running `snakemake` directly, and what their arguments are. 2. Can you run `pwd` ( **p** rint **w** orking **d** irectory) in the same place you’re running the build command above and share what it outputs? I haven’t heard of anyone else using Nextstrain under Cygwin (and I haven’t tried it myself), so let us know how it goes as you proceed! ---
**Author:** ![SophieLuiWi](https://avatars.discourse-cdn.com/v4/letter/s/c77e96/32.png) [@SophieLuiWi](https://nextstrain.discourse.group/u/SophieLuiWi)\ **Post date:** [April 28, 2021, 5:22am UTC](https://nextstrain.discourse.group/t/snakefile-not-found/507/3 "2021-04-28T05:22:12Z")
Hi, thanks a lot! I followed the steps from the “Quickstart” tutorial and am running this command: nextstrain build --cpus 1 zika-tutorial/ I am in the same directory as the zika-tutorial folder, which contains the Snakefile. Could there be a problem with the nextstrain setup? When I do “nextstrain check-setup” I get some error messages, but it all end s with “All good”, so I proceeded. Maybe this screenshot helps: ![nextstrain](https://canada1.discourse-cdn.com/flex031/uploads/nextstrain/original/1X/21503dcad9f17ac0ad0bf800f642e84419eca31a.png) Thanks a lot! I really appreciate your help! ---
**Author:** ![trs](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/trs/32/5_2.png) [@trs](https://nextstrain.discourse.group/u/trs)\ **Post date:** [April 28, 2021, 6:10pm UTC](https://nextstrain.discourse.group/t/snakefile-not-found/507/4 "2021-04-28T18:10:12Z")
Hmm. That all looks correct, so I wonder if this is related to Cygwin path handling/munging and its interaction with Docker volume mounts. Can you run `nextstrain shell --exec ls zika-tutorial` and share the output? ---
**Author:** ![SophieLuiWi](https://avatars.discourse-cdn.com/v4/letter/s/c77e96/32.png) [@SophieLuiWi](https://nextstrain.discourse.group/u/SophieLuiWi)\ **Post date:** [April 29, 2021, 6:41am UTC](https://nextstrain.discourse.group/t/snakefile-not-found/507/5 "2021-04-29T06:41:50Z")
Sure! The output is: Entering the Nextstrain build environment Mapped volumes: /nextstrain/build is from /cygdrive/c/cygwin/home/sophi/zika-tutorial Run the command “exit” to leave the build environment. ---
**Author:** ![trs](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/trs/32/5_2.png) [@trs](https://nextstrain.discourse.group/u/trs)\ **Post date:** [April 30, 2021, 4:54pm UTC](https://nextstrain.discourse.group/t/snakefile-not-found/507/6 "2021-04-30T16:54:12Z")
Hmm. So no additional output from `ls`? That’s certainly odd, as it appears the volume mapping into the container isn’t working but also isn’t failing/erroring. I suspect something with Cygwin is implicated here, as it’s not an OS/platform we’ve tested on. ---
**Author:** ![SophieLuiWi](https://avatars.discourse-cdn.com/v4/letter/s/c77e96/32.png) [@SophieLuiWi](https://nextstrain.discourse.group/u/SophieLuiWi)\ **Post date:** [May 3, 2021, 6:27am UTC](https://nextstrain.discourse.group/t/snakefile-not-found/507/7 "2021-05-03T06:27:37Z")
No additional output unfortunately. I will update cygwin again and let you know if that’ll fix the problem. Thanks a lot for you help already!