alevin-fry: ExitStatus(unix_wait_status(6))

I have had this problem when running the simpleaf quant, but I don’t know how to solve it.

(af) anto@NUBIAN:~/Dunja/Anto/AF_SAMPLE_DIR$ simpleaf quant --reads1 $reads1 --reads2 $reads2 --threads 18 --index IDX_DIR/index --chemistry 10xv2 --resolution cr-like --expected-ori fw --unfiltered-pl --t2g-m
ap IDX_DIR/index/t2g_3col.tsv --output AF_SAMPLE_DIR/pbmc1k_quant

2024-03-05T23:40:47.954352Z  INFO simpleaf::simpleaf_commands::quant: piscem map-sc cmd : /home/anto/anaconda3/envs/af/bin/piscem map-sc --index IDX_DIR/index/piscem_idx --threads 18 -o AF_SAMPLE_DIR/pbmc1k_quant/af_map --max-ec-card 4096 --skipping-strategy permissive --max-hit-occ 256 --max-hit-occ-recover 1024 --max-read-occ 2500 -1 FASTQ_DIR/SRR11442128_1.fastq.gz,FASTQ_DIR/SRR11442139_1.fastq.gz,FASTQ_DIR/SRR11442152_1.fastq.gz,FASTQ_DIR/SRR11442163_1.fastq.gz,FASTQ_DIR/SRR11442174_1.fastq.gz,FASTQ_DIR/SRR11442185_1.fastq.gz,FASTQ_DIR/SRR11442196_1.fastq.gz,FASTQ_DIR/SRR11442207_1.fastq.gz,FASTQ_DIR/SRR11442225_1.fastq.gz,FASTQ_DIR/SRR11442226_1.fastq.gz,FASTQ_DIR/SRR11442227_1.fastq.gz,FASTQ_DIR/SRR11442228_1.fastq.gz,FASTQ_DIR/SRR11442229_1.fastq.gz,FASTQ_DIR/SRR11442230_1.fastq.gz,FASTQ_DIR/SRR11442231_1.fastq.gz,FASTQ_DIR/SRR11442232_1.fastq.gz,FASTQ_DIR/SRR11442233_1.fastq.gz,FASTQ_DIR/SRR11442234_1.fastq.gz,FASTQ_DIR/SRR11442235_1.fastq.gz,FASTQ_DIR/SRR11442244_1.fastq.gz,FASTQ_DIR/SRR11442255_1.fastq.gz,FASTQ_DIR/SRR11442256_1.fastq.gz,FASTQ_DIR/SRR11442257_1.fastq.gz -2 FASTQ_DIR/SRR11442128_2.fastq.gz,FASTQ_DIR/SRR11442139_2.fastq.gz,FASTQ_DIR/SRR11442152_2.fastq.gz,FASTQ_DIR/SRR11442163_2.fastq.gz,FASTQ_DIR/SRR11442174_2.fastq.gz,FASTQ_DIR/SRR11442185_2.fastq.gz,FASTQ_DIR/SRR11442196_2.fastq.gz,FASTQ_DIR/SRR11442207_2.fastq.gz,FASTQ_DIR/SRR11442225_2.fastq.gz,FASTQ_DIR/SRR11442226_2.fastq.gz,FASTQ_DIR/SRR11442227_2.fastq.gz,FASTQ_DIR/SRR11442228_2.fastq.gz,FASTQ_DIR/SRR11442229_2.fastq.gz,FASTQ_DIR/SRR11442230_2.fastq.gz,FASTQ_DIR/SRR11442231_2.fastq.gz,FASTQ_DIR/SRR11442232_2.fastq.gz,FASTQ_DIR/SRR11442233_2.fastq.gz,FASTQ_DIR/SRR11442234_2.fastq.gz,FASTQ_DIR/SRR11442235_2.fastq.gz,FASTQ_DIR/SRR11442244_2.fastq.gz,FASTQ_DIR/SRR11442255_2.fastq.gz,FASTQ_DIR/SRR11442256_2.fastq.gz,FASTQ_DIR/SRR11442257_2.fastq.gz --geometry chromium_v2
2024-03-05T23:48:17.223557Z ERROR simpleaf::utils::prog_utils: command unsuccessful (signal: 6 (SIGABRT)): "/home/anto/anaconda3/envs/af/bin/piscem" "map-sc" "--index" "IDX_DIR/index/piscem_idx" "--threads" "18" "-o" "AF_SAMPLE_DIR/pbmc1k_quant/af_map" "--max-ec-card" "4096" "--skipping-strategy" "permissive" "--max-hit-occ" "256" "--max-hit-occ-recover" "1024" "--max-read-occ" "2500" "-1" "FASTQ_DIR/SRR11442128_1.fastq.gz,FASTQ_DIR/SRR11442139_1.fastq.gz,FASTQ_DIR/SRR11442152_1.fastq.gz,FASTQ_DIR/SRR11442163_1.fastq.gz,FASTQ_DIR/SRR11442174_1.fastq.gz,FASTQ_DIR/SRR11442185_1.fastq.gz,FASTQ_DIR/SRR11442196_1.fastq.gz,FASTQ_DIR/SRR11442207_1.fastq.gz,FASTQ_DIR/SRR11442225_1.fastq.gz,FASTQ_DIR/SRR11442226_1.fastq.gz,FASTQ_DIR/SRR11442227_1.fastq.gz,FASTQ_DIR/SRR11442228_1.fastq.gz,FASTQ_DIR/SRR11442229_1.fastq.gz,FASTQ_DIR/SRR11442230_1.fastq.gz,FASTQ_DIR/SRR11442231_1.fastq.gz,FASTQ_DIR/SRR11442232_1.fastq.gz,FASTQ_DIR/SRR11442233_1.fastq.gz,FASTQ_DIR/SRR11442234_1.fastq.gz,FASTQ_DIR/SRR11442235_1.fastq.gz,FASTQ_DIR/SRR11442244_1.fastq.gz,FASTQ_DIR/SRR11442255_1.fastq.gz,FASTQ_DIR/SRR11442256_1.fastq.gz,FASTQ_DIR/SRR11442257_1.fastq.gz" "-2" "FASTQ_DIR/SRR11442128_2.fastq.gz,FASTQ_DIR/SRR11442139_2.fastq.gz,FASTQ_DIR/SRR11442152_2.fastq.gz,FASTQ_DIR/SRR11442163_2.fastq.gz,FASTQ_DIR/SRR11442174_2.fastq.gz,FASTQ_DIR/SRR11442185_2.fastq.gz,FASTQ_DIR/SRR11442196_2.fastq.gz,FASTQ_DIR/SRR11442207_2.fastq.gz,FASTQ_DIR/SRR11442225_2.fastq.gz,FASTQ_DIR/SRR11442226_2.fastq.gz,FASTQ_DIR/SRR11442227_2.fastq.gz,FASTQ_DIR/SRR11442228_2.fastq.gz,FASTQ_DIR/SRR11442229_2.fastq.gz,FASTQ_DIR/SRR11442230_2.fastq.gz,FASTQ_DIR/SRR11442231_2.fastq.gz,FASTQ_DIR/SRR11442232_2.fastq.gz,FASTQ_DIR/SRR11442233_2.fastq.gz,FASTQ_DIR/SRR11442234_2.fastq.gz,FASTQ_DIR/SRR11442235_2.fastq.gz,FASTQ_DIR/SRR11442244_2.fastq.gz,FASTQ_DIR/SRR11442255_2.fastq.gz,FASTQ_DIR/SRR11442256_2.fastq.gz,FASTQ_DIR/SRR11442257_2.fastq.gz" "--geometry" "chromium_v2"

2024-03-05T23:48:17.223640Z ERROR simpleaf::utils::prog_utils: stderr :
====

2024-03-05T23:40:48.000699Z  INFO piscem: cmd: ["sc_ref_mapper", "-i", "IDX_DIR/index/piscem_idx", "-g", "chromium_v2", "-1", 
"FASTQ_DIR/SRR11442128_1.fastq.gz,FASTQ_DIR/SRR11442139_1.fastq.gz,FASTQ_DIR/SRR11442152_1.fastq.gz,FASTQ_DIR/SRR11442163_1.fastq.gz,FASTQ_DIR/SRR11442174_1.fastq.gz,FASTQ_DIR/SRR11442185_1.fastq.gz,FASTQ_DIR/SRR11442196_1.fastq.gz,FASTQ_DIR/SRR11442207_1.fastq.gz,FASTQ_DIR/SRR11442225_1.fastq.gz,FASTQ_DIR/SRR11442226_1.fastq.gz,FASTQ_DIR/SRR11442227_1.fastq.gz,FASTQ_DIR/SRR11442228_1.fastq.gz,FASTQ_DIR/SRR11442229_1.fastq.gz,FASTQ_DIR/SRR11442230_1.fastq.gz,FASTQ_DIR/SRR11442231_1.fastq.gz,FASTQ_DIR/SRR11442232_1.fastq.gz,FASTQ_DIR/SRR11442233_1.fastq.gz,FASTQ_DIR/SRR11442234_1.fastq.gz,FASTQ_DIR/SRR11442235_1.fastq.gz,FASTQ_DIR/SRR11442244_1.fastq.gz,FASTQ_DIR/SRR11442255_1.fastq.gz,FASTQ_DIR/SRR11442256_1.fastq.gz,FASTQ_DIR/SRR11442257_1.fastq.gz", "-2", "FASTQ_DIR/SRR11442128_2.fastq.gz,FASTQ_DIR/SRR11442139_2.fastq.gz,FASTQ_DIR/SRR11442152_2.fastq.gz,FASTQ_DIR/SRR11442163_2.fastq.gz,FASTQ_DIR/SRR11442174_2.fastq.gz,FASTQ_DIR/SRR11442185_2.fastq.gz,FASTQ_DIR/SRR11442196_2.fastq.gz,FASTQ_DIR/SRR11442207_2.fastq.gz,FASTQ_DIR/SRR11442225_2.fastq.gz,FASTQ_DIR/SRR11442226_2.fastq.gz,FASTQ_DIR/SRR11442227_2.fastq.gz,FASTQ_DIR/SRR11442228_2.fastq.gz,FASTQ_DIR/SRR11442229_2.fastq.gz,FASTQ_DIR/SRR11442230_2.fastq.gz,FASTQ_DIR/SRR11442231_2.fastq.gz,FASTQ_DIR/SRR11442232_2.fastq.gz,FASTQ_DIR/SRR11442233_2.fastq.gz,FASTQ_DIR/SRR11442234_2.fastq.gz,FASTQ_DIR/SRR11442235_2.fastq.gz,FASTQ_DIR/SRR11442244_2.fastq.gz,FASTQ_DIR/SRR11442255_2.fastq.gz,FASTQ_DIR/SRR11442256_2.fastq.gz,FASTQ_DIR/SRR11442257_2.fastq.gz", "-t", "18", "-o", "AF_SAMPLE_DIR/pbmc1k_quant/af_map", "--max-ec-card", "4096", "--skipping-strategy", "permissive", "--max-hit-occ", "256", "--max-hit-occ-recover", "1024", "--max-read-occ", "2500"]

[2024-03-06 00:40:48.000] [info] enable structural constraints : false

[2024-03-06 00:40:48.000] [info] No poison k-mer map exists, or it was requested not to be used

[2024-03-06 00:40:48.000] [info] loading index from IDX_DIR/index/piscem_idx

[2024-03-06 00:40:49.420] [info] done loading index

processed (212500000) reads; (170651220) had mappings.fatal runtime error: Rust cannot catch foreign exceptions
====

Error: piscem mapping failed with exit status ExitStatus(unix_wait_status(6))

About this issue

Original URL
State: closed
Created 4 months ago
Comments: 24 (11 by maintainers)

Most upvoted comments

Thank you very much, everything solved.

I was using cellranger before starting with alevin-fry, and the output off cellranger are different documenta that I can use to feed drolpetqc and decontx but now i Will use you explanation for doing the qc.

Thank you very much.

El sáb, 9 mar 2024, 2:57, Dongze He @.***> escribió:

Hi @Anto9393 https://github.com/Anto9393, According to dropletQC, nuclear fraction is defined as

nuclear fraction = intronic reads / (intronic reads + exonic reads)

Yes. You can load the quantification result of alevin-fry into R using the loadFry function from fishpond https://bioconductor.org/packages/release/bioc/html/fishpond.html. You will need to specify the outputFormat=scrna. This will assign all exonic UMIs as spliced UMIs. loafFry returns a SingleCellExperiment object containing two assays (count matrices),Spliced and Unspliced. You can use these two count matrices to compute the nuclear fraction. To be specific, you need to compute the colSums of the two count matrices to get the spliced(exonic) and unspliced(intronic) total count of each cell. The nuclear fraction can then be computed by dividing the colSums results of the two count matrices.

The above answer was based on the definition of nuclear fraction. I did not dig into their code to see how they calculate the nuclear fraction. One more thing is that we recommend to use the emptyDrops function from DropletUtils https://bioconductor.org/packages/release/bioc/html/DropletUtils.html to detect high-quality cells.

Finally, I am not sure what you mean by I was using the cellranger output. The above answer only works for alevin-fry results, because cellranger cannot return spliced and unspliced count separately.

Best, Dongze

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Anto9393 on Mar 9, 2024

Thank you very much it works perfectly now. Just for ending the issue, is there a way to quantify the nuclear fraction on the cells? since now I was using the cellranger output and dropletqc thanks

Anto9393 on Mar 9, 2024

in the wsl there is not partition, maybe that the problem. I will try with linux

Anto9393 on Mar 6, 2024