Error while aligning 10X CRISPR 5' screening scRNAseq data

[eynullazada]

Hi

I am getting the following error when aligning my 5' 10X CRISPR scRNAseq data using alevin fry:

/mnt/dv/wid/projects6/Roy-singlecell3/sridharanlab2/data/perturb-seq_on_reprogramming/fastq/GEX/GEX_1_S1_L008_R2_001.fastq.gz" "--geometry" "chromium_v3" 2024-07-02T05:21:00.955265Z ERROR simpleaf::utils::prog_utils: stderr :

2024-07-02T05:20:46.942187Z INFO piscem: cmd: ["sc_ref_mapper", "-i", "alevin_fry_alignment2/gene_expression/simpleaf_index/index/piscem_idx", "-g", "chromium_v3", "-1", "/mnt/dv/wid/projects6/Roy-singlecell3/sridharanlab2/data/perturb-seq_on_reprogramming/fastq/GEX/

GEX_1_S1_L008_R2_001.fastq.gz", "-t", "16", "-o", "alevin_fry_alignment2/gene_expression/simpleaf_quant/af_map", "--max-ec-card", "4096", "--skipping-strategy", "permissive", "--max-hit-occ", "256", "--max-hit-occ-recover", "1024", "--max-read-occ", "2500"] [2024-07-02 00:20:46.963] [info] enable structural constraints : false [2024-07-02 00:20:46.966] [info] No poison k-mer map exists, or it was requested not to be used [2024-07-02 00:20:46.966] [info] loading index from alevin_fry_alignment2/gene_expression/simpleaf_index/index/piscem_idx [2024-07-02 00:21:00.232] [info] done loading index fatal runtime error: Rust cannot catch foreign exceptions

2024-07-02T05:21:00.962190Z INFO simpleaf::utils::workflow_utils: Execution terminated at "simpleaf quant" command for step 2 Error: piscem mapping failed with exit status ExitStatus(unix_wait_status(134))

[rob-p]

Hi @eynullazada,

Thanks for reporting the issue. Can you let us know what system you are running on (e.g. which distribution of linux and version) and what version of simpleaf, piscem and alevin-fry you have installed, and also the specific full command you are invoking?

There seem to be some strange formatting issues with the output posted above that make it difficult to parse, but we can work backward from the specific invocation to try and figure out what might be going awry. cc @DongzeHE

--Rob

[eynullazada]

Hi Rob

Thanks for quick response. I am running it in linux environment:

NAME="CentOS Linux" VERSION="7 (Core)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (Core)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:7" HOME_URL="https://www.centos.org/" BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7" CENTOS_MANTISBT_PROJECT_VERSION="7" REDHAT_SUPPORT_PRODUCT="centos" REDHAT_SUPPORT_PRODUCT_VERSION="7"

Versions are like this: simpleaf 0.16.2 alevin-fry 0.9.0 piscem 0.8.0

And command is like this:

impleaf workflow run --template simpleaf/10x-feature-barcode-crispr_template/10x-feature-barcode-crispr.jsonnet --output alevin_fry_alignment

I am looking forward to hearing from you.

Khagani

---

From: Rob Patro @.> Sent: Tuesday, July 9, 2024 3:17 PM To: COMBINE-lab/alevin-fry @.> Cc: KHAGANI EYNULLAZADA @.>; Mention @.> Subject: Re: [COMBINE-lab/alevin-fry] Error while aligning 10X CRISPR 5' screening scRNAseq data (Issue #145)

Hi @eynullazadahttps://urldefense.com/v3/__https://github.com/eynullazada__;!!Mak6IKo!ORPI5M9Ud5rsIPjg9h8g8pa-SXKQIdCtoAgRKEClXXTVaMw2yLfqWw8FxX744MQKy87C87fiFuqS-qDl9TeZ8IKNxyRD$,

Thanks for reporting the issue. Can you let us know what system you are running on (e.g. which distribution of linux and version) and what version of simpleaf, piscem and alevin-fry you have installed, and also the specific full command you are invoking?

There seem to be some strange formatting issues with the output posted above that make it difficult to parse, but we can work backward from the specific invocation to try and figure out what might be going awry. cc @DongzeHEhttps://urldefense.com/v3/__https://github.com/DongzeHE__;!!Mak6IKo!ORPI5M9Ud5rsIPjg9h8g8pa-SXKQIdCtoAgRKEClXXTVaMw2yLfqWw8FxX744MQKy87C87fiFuqS-qDl9TeZ8DNJB1n4$

--Rob

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/COMBINE-lab/alevin-fry/issues/145*issuecomment-2218655384__;Iw!!Mak6IKo!ORPI5M9Ud5rsIPjg9h8g8pa-SXKQIdCtoAgRKEClXXTVaMw2yLfqWw8FxX744MQKy87C87fiFuqS-qDl9TeZ8BMUpI5j$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ANGUEUZWIQM5WORCU576YJDZLRANXAVCNFSM6AAAAABKTNMDKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJYGY2TKMZYGQ__;!!Mak6IKo!ORPI5M9Ud5rsIPjg9h8g8pa-SXKQIdCtoAgRKEClXXTVaMw2yLfqWw8FxX744MQKy87C87fiFuqS-qDl9TeZ8AzdjRmD$. You are receiving this because you were mentioned.

[eynullazada]

Hi Rob

Just to reminder that I am still looking forward to hearing from you on this issue. Thanks

Khagani

[rob-p]

Hi @eynullazada, thanks for the reminder. Is there any small subset of the data you might be able to share? Also, could you please try upgrading to the latest versions of simpleaf, piscem, and alevin-fry?

I’ll also cc @DongzeHE who is the workflow expert here!

[eynullazada]

Hi Rob

I can share fastq files. but what is the best way of sharing it?

Khagani

[rob-p]

Hi Khagani,

If you have an FTP or a Google Drive where you can share, you can link here (or send an e-mail if you don't want to post such a link publicly). Alternatively, something like globus (https://www.globus.org/) would also work if you have an account there.

--Rob

[DongzeHE]

Hi Khagani,

Could you also share the logs generated by simpleaf workflow? The two _log.json files should be in the output directory you specified, i.e., alevin_fry_alignment. Thanks.

Best, Dongze