# Problem with Setup **URL:** \ **Category:** Help and Getting Started\ **Created:** [October 22, 2021, 3:23am UTC](https://nextstrain.discourse.group/t/problem-with-setup/783 "2021-10-22T03:23:52Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![rajannepal048](https://avatars.discourse-cdn.com/v4/letter/r/ed655f/32.png) [@rajannepal048](https://nextstrain.discourse.group/u/rajannepal048)\ **Post date:** [October 22, 2021, 3:23am UTC](https://nextstrain.discourse.group/t/problem-with-setup/783/1 "2021-10-22T03:23:52Z")
I am using WSL (Ubuntu) to run nextstrain. When I was running the last command _nextstrain build . --cores 4 --use-conda \* \*\* --configfile ./my\_profiles/getting\_started/builds.yaml_\* and snakemake --profile my\_profiles/getting\_started -p And I am getting the following error. Error in rule align: jobid: 11 output: results/aligned\_example-data.fasta.xz, results/insertions\_example-data.tsv, results/translations/seqs\_example-data.gene.ORF1a.fasta.xz, results/translations/seqs\_example-data.gene.ORF1b.fasta.xz, results/translations/seqs\_example-data.gene.S.fasta.xz, results/translations/seqs\_example-data.gene.ORF3a.fasta.xz, results/translations/seqs\_example-data.gene.E.fasta.xz, results/translations/seqs\_example-data.gene.M.fasta.xz, results/translations/seqs\_example-data.gene.ORF6.fasta.xz, results/translations/seqs\_example-data.gene.ORF7a.fasta.xz, results/translations/seqs\_example-data.gene.ORF7b.fasta.xz, results/translations/seqs\_example-data.gene.ORF8.fasta.xz, results/translations/seqs\_example-data.gene.N.fasta.xz, results/translations/seqs\_example-data.gene.ORF9b.fasta.xz log: logs/align\_example-data.txt (check log file(s) for error message) shell: ``` python3 scripts/sanitize_sequences.py --sequences data/example_sequences.fasta.gz --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout 2> logs/sanitize_sequences_example-data.txt | nextalign --jobs=1 --reference defaults/reference_seq.fasta --genemap defaults/annotation.gff --genes ORF1a,ORF1b,S,ORF3a,E,M,ORF6,ORF7a,ORF7b,ORF8,N,ORF9b --sequences /dev/stdin --output-dir results/translations --output-basename seqs_example-data --output-fasta results/aligned_example-data.fasta --output-insertions results/insertions_example-data.tsv > logs/align_example-data.txt 2>&1; xz -2 results/aligned_example-data.fasta; xz -2 results/translations/seqs_example-data*.fasta (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) ``` Logfile logs/align\_example-data.txt: [WARN] Nextalign: Warning: in sequence “USA/UT-01231/2020”: When processing gene “ORF7b”: Unable to align: no seed matches. Note that this gene will not be included in the results of the sequence. What should I do? ---
**Author:** ![james](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/james/32/11_2.png) [@james](https://nextstrain.discourse.group/u/james)\ **Post date:** [October 24, 2021, 9:32pm UTC](https://nextstrain.discourse.group/t/problem-with-setup/783/2 "2021-10-24T21:32:58Z")
Hi @rajannepal - is that the only content in `logs/align_example-data.txt`? That message alone shouldn’t cause the command to fail. P.S. If you are running `nextstrain build` using a docker container, [please avoid using `--use-conda`](https://nextstrain.discourse.group/t/installation-issue/626/2) ---
**Author:** ![rajannepal048](https://avatars.discourse-cdn.com/v4/letter/r/ed655f/32.png) [@rajannepal048](https://nextstrain.discourse.group/u/rajannepal048)\ **Post date:** [October 26, 2021, 1:52am UTC](https://nextstrain.discourse.group/t/problem-with-setup/783/3 "2021-10-26T01:52:16Z")
Hi @james , I am using WSL (Ubuntu). As you mentioned I have found another error ![Capture](https://canada1.discourse-cdn.com/flex031/uploads/nextstrain/original/1X/2a7a09a0eb027525e3dee67ece47ede342d702b4.png) Job 11: Aligning sequences to defaults/reference\_seq.fasta - gaps relative to reference are considered real ``` python3 scripts/sanitize_sequences.py --sequences data/example_sequences.fasta.gz --strip-prefixes hCoV-19/ SARS-CoV-2/ --output /dev/stdout 2> logs/sanitize_sequences_example-data.txt | nextalign --jobs=1 --reference defaults/reference_seq.fasta --genemap defaults/annotation.gff --genes ORF1a,ORF1b,S,ORF3a,E,M,ORF6,ORF7a,ORF7b,ORF8,N,ORF9b --sequences /dev/stdin --output-dir results/translations --output-basename seqs_example-data --output-fasta results/aligned_example-data.fasta --output-insertions results/insertions_example-data.tsv > logs/align_example-data.txt 2>&1; xz -2 results/aligned_example-data.fasta; xz -2 results/translations/seqs_example-data*.fasta ``` **xz: results/aligned\_example-data.fasta.xz: Cannot set the file permissions: Operation not permitted** ---
**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:** [October 26, 2021, 9:45pm UTC](https://nextstrain.discourse.group/t/problem-with-setup/783/4 "2021-10-26T21:45:25Z")
This error message: > [@rajannepal048](#): > > xz: results/aligned\_example-data.fasta.xz: Cannot set the file permissions: Operation not permitted combined with the workflow path from your screenshot: ``` /mnt/r/ncov/… ``` suggests to me that `xz` thinks its on a POSIX filesystem (e.g. Linux, macOS) but is actually on some other filesystem which doesn’t support POSIX file permissions. Probably a Windows drive path mounted into WSL at `/mnt/r`? Can you try the workaround of using a non-Windows path in WSL? (I’m not personally familiar enough with WSL to be more specific here…) Trying that out will at least let us verify the cause of the issue, even if it’s not an ideal solution. ---
**Author:** ![rajannepal048](https://avatars.discourse-cdn.com/v4/letter/r/ed655f/32.png) [@rajannepal048](https://nextstrain.discourse.group/u/rajannepal048)\ **Post date:** [October 28, 2021, 2:08am UTC](https://nextstrain.discourse.group/t/problem-with-setup/783/5 "2021-10-28T02:08:39Z")
@trs I already tried in POSIX file system and it works. And it does not work on r because of the windows file system. ---
**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:** [October 29, 2021, 11:05pm UTC](https://nextstrain.discourse.group/t/problem-with-setup/783/6 "2021-10-29T23:05:42Z")
Got it. Thanks for following up, @rajannepal048! I’m glad it’s working for you now.