Running mulit_snp on focusscope data leads to error in later stages

[jaspitzer]

Describe the bug

When running multi_snp, the later stages seem to fail

It's really hard to give instructions for reproducibility, as you probably do not have access to my data and I don't know whats causing the error.

the mapfile:
C221220003_FOC PBMC_20210209_Sample_ID_C221220003/fastq tet2_foc tet2
C221220002_FOC PBMC_20211012_Sample_ID_C221220002/fastq dnmt3a_foc dnmt3a
C221220001_FOC PBMC_20220404_Sample_ID_C221220001/fastq jak2_foc jak2

input:
multi_snp
--mapfile ./mapfile_foc.txt
--genomeDir ../hs_ensembl_99
--thread 12
--mod shell
--gene_list gene_list.txt
--ref_threshold_method none
--alt_threshold_method none
--not_consensus

error:
00:00:19 Predicting variants

WARNINGS: Some warning were detected
Warning type Number of warnings
WARNING_TRANSCRIPT_INCOMPLETE 94
WARNING_TRANSCRIPT_NO_START_CODON 8
WARNING_TRANSCRIPT_NO_STOP_CODON 19

00:00:22 Creating summary file: snpEff_summary.html
00:00:22 Creating genes file: snpEff_genes.txt
00:00:22 done.
00:00:22 Logging
00:00:23 Checking for updates...
00:00:24 Done.
2023-06-27 12:16:27,525 - celescope.snp.analysis_snp.run_snpEff - INFO - done. time used: 0:00:25.109783
2023-06-27 12:16:27,526 - celescope.snp.analysis_snp.keep_in_gene - INFO - start...
2023-06-27 12:16:28,163 - celescope.snp.analysis_snp.keep_in_gene - INFO - done. time used: 0:00:00.637491
2023-06-27 12:16:28,163 - celescope.snp.analysis_snp.write_gt - INFO - start...
2023-06-27 12:16:28,164 - celescope.tools.step.debug_subprocess_call - INFO - start...
2023-06-27 12:16:28,164 - celescope.tools.step.debug_subprocess_call - INFO - Rscript /home/js/mambaforge/envs/celescope/lib/python3.9/site-packages/celescope/snp/vcfR.R --vcf .//tet2_foc/09.analysis_snp/tet2_foc_final.vcf --out .//tet2_foc/09.analysis_snp/tet2_foc_gt.csv 2>&1

***** *** vcfR *** *****
This is vcfR 1.13.0
browseVignettes('vcfR') # Documentation
citation('vcfR') # Citation

---

2023-06-27 12:16:34,180 - celescope.tools.step.debug_subprocess_call - INFO - done. time used: 0:00:06.016181
2023-06-27 12:16:34,180 - celescope.snp.analysis_snp.write_gt - INFO - done. time used: 0:00:06.016441
2023-06-27 12:16:34,180 - celescope.snp.analysis_snp.write_ncell - INFO - start...
2023-06-27 12:16:35,613 - celescope.snp.analysis_snp.write_ncell - INFO - done. time used: 0:00:01.433084
2023-06-27 12:16:36,136 - celescope.snp.analysis_snp.plot_snp - INFO - start...
2023-06-27 12:16:36,136 - celescope.tools.utils.parse_match_dir - INFO - start...
2023-06-27 12:16:36,136 - celescope.tools.utils.get_matrix_dir_from_match_dir - INFO - start...
2023-06-27 12:16:36,137 - celescope.tools.utils.get_matrix_dir_from_match_dir - INFO - Matrix_dir :tet2/05.count/tet2_filtered_feature_bc_matrix
2023-06-27 12:16:36,137 - celescope.tools.utils.get_matrix_dir_from_match_dir - INFO - done. time used: 0:00:00.000292
2023-06-27 12:16:36,137 - celescope.tools.utils.get_barcode_from_match_dir - INFO - start...
2023-06-27 12:16:36,137 - celescope.tools.utils.get_matrix_dir_from_match_dir - INFO - start...
2023-06-27 12:16:36,137 - celescope.tools.utils.get_matrix_dir_from_match_dir - INFO - Matrix_dir :tet2/05.count/tet2_filtered_feature_bc_matrix
2023-06-27 12:16:36,137 - celescope.tools.utils.get_matrix_dir_from_match_dir - INFO - done. time used: 0:00:00.000092
2023-06-27 12:16:36,137 - celescope.tools.utils.get_barcode_from_matrix_dir - INFO - start...
2023-06-27 12:16:36,142 - celescope.tools.utils.get_barcode_from_matrix_dir - INFO - done. time used: 0:00:00.004704
2023-06-27 12:16:36,142 - celescope.tools.utils.get_barcode_from_match_dir - INFO - done. time used: 0:00:00.004919
2023-06-27 12:16:36,142 - celescope.tools.utils.parse_match_dir - INFO - done. time used: 0:00:00.005884
2023-06-27 12:16:37,162 - celescope.tools.step._clean_up - INFO - start...
2023-06-27 12:16:37,163 - celescope.tools.step._render_html - INFO - start...
2023-06-27 12:16:37,475 - celescope.tools.step.render_html - INFO - done. time used: 0:00:00.312702
2023-06-27 12:16:37,476 - celescope.tools.step.clean_up - INFO - done. time used: 0:00:00.313805
Traceback (most recent call last):
File "/home/js/mambaforge/envs/celescope/bin/celescope", line 8, in
sys.exit(main())
File "/home/js/mambaforge/envs/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 43, in main
args.func(args)
File "/home/js/mambaforge/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 46, in wrapper
result = func(*args, **kwargs)
File "/home/js/mambaforge/envs/celescope/lib/python3.9/site-packages/celescope/snp/analysis_snp.py", line 307, in analysis_snp
runner.run()
File "/home/js/mambaforge/envs/celescope/lib/python3.9/site-packages/celescope/snp/analysis_snp.py", line 299, in run
self.plot_snp()
File "/home/js/mambaforge/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 46, in wrapper
result = func(*args, **kwargs)
File "/home/js/mambaforge/envs/celescope/lib/python3.9/site-packages/celescope/snp/analysis_snp.py", line 278, in plot_snp
indices = [int(x.split('')[2])-1 for x in variants]
File "/home/js/mambaforge/envs/celescope/lib/python3.9/site-packages/celescope/snp/analysis_snp.py", line 278, in
indices = [int(x.split('')[2])-1 for x in variants]
IndexError: list index out of range

conda list output:

packages in environment at /home/js/mambaforge/envs/celescope:

Name Version Build Channel

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r-miniui 0.1.1.1 r40hc72bb7e_1002 conda-forge
r-modelr 0.1.9 r40hc72bb7e_0 conda-forge
r-munsell 0.5.0 r40hc72bb7e_1004 conda-forge
r-nlme 3.1_159 r40h8da6f51_0 conda-forge
r-npsurv 0.5_0 r40hc72bb7e_0 conda-forge
r-openssl 2.0.3 r40hfaab4ff_0 conda-forge
r-parallelly 1.32.1 r40hc72bb7e_0 conda-forge
r-patchwork 1.1.2 r40hc72bb7e_0 conda-forge
r-pbapply 1.5_0 r40hc72bb7e_0 conda-forge
r-permute 0.9_7 r40hc72bb7e_0 conda-forge
r-pillar 1.8.1 r40hc72bb7e_0 conda-forge
r-pinfsc50 1.2.0 r40ha770c72_0 conda-forge
r-pkgconfig 2.0.3 r40hc72bb7e_1 conda-forge
r-pkgload 1.3.0 r40hc72bb7e_0 conda-forge
r-plotly 4.10.0 r40hc72bb7e_0 conda-forge
r-plyr 1.8.7 r40h7525677_0 conda-forge
r-png 0.1_7 r40hcfec24a_1004 conda-forge
r-polyclip 1.10_0 r40h7525677_2 conda-forge
r-praise 1.0.0 r40hc72bb7e_1005 conda-forge
r-prettyunits 1.1.1 r40hc72bb7e_1 conda-forge
r-processx 3.7.0 r40h06615bd_0 conda-forge
r-progress 1.2.2 r40hc72bb7e_2 conda-forge
r-progressr 0.11.0 r40hc72bb7e_0 conda-forge
r-promises 1.2.0.1 r40h03ef668_0 conda-forge
r-ps 1.7.1 r40h06615bd_0 conda-forge
r-purrr 0.3.4 r40hcfec24a_1 conda-forge
r-r6 2.5.1 r40hc72bb7e_0 conda-forge
r-rann 2.6.1 r40h7525677_2 conda-forge
r-rappdirs 0.3.3 r40hcfec24a_0 conda-forge
r-rcolorbrewer 1.1_3 r40h785f33e_0 conda-forge
r-rcpp 1.0.9 r40h7525677_1 conda-forge
r-rcppannoy 0.0.19 r40h7525677_0 conda-forge
r-rcpparmadillo 0.11.2.3.1 r40h9f5de39_0 conda-forge
r-rcppeigen 0.3.3.9.2 r40h43535f1_0 conda-forge
r-rcppparallel 5.1.5 r40h7525677_0 conda-forge
r-rcppprogress 0.4.2 r40hc72bb7e_1 conda-forge
r-rcpptoml 0.1.7 r40h03ef668_1 conda-forge
r-readr 2.1.2 r40h03ef668_0 conda-forge
r-readxl 1.4.1 r40hf23e330_0 conda-forge
r-rematch 1.0.1 r40hc72bb7e_1004 conda-forge
r-rematch2 2.1.2 r40hc72bb7e_1 conda-forge
r-reprex 2.0.2 r40hc72bb7e_0 conda-forge
r-reshape2 1.4.4 r40h03ef668_1 conda-forge
r-reticulate 1.28 r40h38f115c_0 conda-forge
r-rgeos 0.5_9 r40hf730bdb_3 conda-forge
r-rlang 1.0.6 r40h7525677_0 conda-forge
r-rmarkdown 2.16 r40hc72bb7e_0 conda-forge
r-rocr 1.0_11 r40hc72bb7e_1 conda-forge
r-rpart 4.1.16 r40hcfec24a_0 conda-forge
r-rprojroot 2.0.3 r40hc72bb7e_0 conda-forge
r-rspectra 0.16_1 r40h9f5de39_0 conda-forge
r-rstudioapi 0.14 r40hc72bb7e_0 conda-forge
r-rtsne 0.16 r40h37cf8d7_0 conda-forge
r-rvest 1.0.3 r40hc72bb7e_0 conda-forge
r-sass 0.4.2 r40h7525677_0 conda-forge
r-scales 1.2.1 r40hc72bb7e_0 conda-forge
r-scattermore 0.8 r40h06615bd_0 conda-forge
r-sctransform 0.3.4 r40hef8c1a7_0 conda-forge
r-selectr 0.4_2 r40hc72bb7e_1 conda-forge
r-seurat 4.0.1 r40h03ef668_0 conda-forge
r-seuratobject 4.1.1 r40h7525677_0 conda-forge
r-shiny 1.7.2 r40h785f33e_0 conda-forge
r-sitmo 2.0.2 r40h7525677_0 conda-forge
r-sourcetools 0.1.7 r40h03ef668_1002 conda-forge
r-sp 1.5_0 r40h06615bd_0 conda-forge
r-spatstat 2.3_4 r40hc72bb7e_0 conda-forge
r-spatstat.core 2.4_4 r40h7525677_0 conda-forge
r-spatstat.data 2.2_0 r40hc72bb7e_0 conda-forge
r-spatstat.geom 2.4_0 r40h06615bd_0 conda-forge
r-spatstat.linnet 2.3_2 r40hcfec24a_0 conda-forge
r-spatstat.random 2.2_0 r40h7525677_0 conda-forge
r-spatstat.sparse 2.1_1 r40h06615bd_0 conda-forge
r-spatstat.utils 2.3_1 r40h06615bd_0 conda-forge
r-stringi 1.7.6 r40hcabe038_0 conda-forge
r-stringr 1.4.1 r40hc72bb7e_0 conda-forge
r-survival 3.4_0 r40h06615bd_0 conda-forge
r-sys 3.4 r40hcfec24a_0 conda-forge
r-tensor 1.5 r40hc72bb7e_1003 conda-forge
r-testthat 3.1.4 r40h7525677_0 conda-forge
r-tibble 3.1.8 r40h06615bd_0 conda-forge
r-tidyr 1.2.1 r40h7525677_0 conda-forge
r-tidyselect 1.1.2 r40hc72bb7e_0 conda-forge
r-tidyverse 1.3.2 r40hc72bb7e_0 conda-forge
r-tinytex 0.42 r40hc72bb7e_0 conda-forge
r-tzdb 0.3.0 r40h7525677_0 conda-forge
r-utf8 1.2.2 r40hcfec24a_0 conda-forge
r-uuid 1.1_0 r40h06615bd_0 conda-forge
r-uwot 0.1.14 r40h7525677_0 conda-forge
r-vcfr 1.13.0 r40h690469d_0 conda-forge
r-vctrs 0.4.1 r40h7525677_0 conda-forge
r-vegan 2.6_2 r40he5c027b_0 conda-forge
r-viridislite 0.4.1 r40hc72bb7e_0 conda-forge
r-vroom 1.5.7 r40h03ef668_0 conda-forge
r-waldo 0.4.0 r40hc72bb7e_0 conda-forge
r-withr 2.5.0 r40hc72bb7e_0 conda-forge
r-xfun 0.33 r40h7525677_0 conda-forge
r-xml2 1.3.3 r40h03ef668_0 conda-forge
r-xtable 1.8_4 r40hc72bb7e_3 conda-forge
r-yaml 2.3.5 r40h06615bd_0 conda-forge
r-zoo 1.8_11 r40h06615bd_0 conda-forge
readline 8.2 h8228510_1 conda-forge
samtools 1.16.1 h00cdaf9_2 bioconda
scanpy 1.8.2 pypi_0 pypi
scikit-learn 1.2.2 pypi_0 pypi
scipy 1.10.1 pypi_0 pypi
seaborn 0.12.2 pypi_0 pypi
sed 4.8 he412f7d_0 conda-forge
setuptools 67.7.2 pyhd8ed1ab_0 conda-forge
sinfo 0.3.4 pypi_0 pypi
six 1.16.0 pypi_0 pypi
snpeff 5.1 hdfd78af_2 bioconda
sorted-nearest 0.0.39 pypi_0 pypi
sqlite 3.42.0 h2c6b66d_0 conda-forge
star 2.6.1b 0 bioconda
statsmodels 0.14.0 pypi_0 pypi
stdlib-list 0.8.0 pypi_0 pypi
subread 2.0.1 h7132678_2 bioconda
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tables 3.8.0 pypi_0 pypi
tabulate 0.9.0 pypi_0 pypi
tenacity 8.2.2 pypi_0 pypi
texttable 1.6.7 pypi_0 pypi
threadpoolctl 3.1.0 pypi_0 pypi
tk 8.6.12 h27826a3_0 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
tomli 2.0.1 pypi_0 pypi
tqdm 4.65.0 pypi_0 pypi
trust4 1.0.7 h5b5514e_0 bioconda
tzdata 2023c h71feb2d_0 conda-forge
umap-learn 0.5.3 pypi_0 pypi
venn 0.1.3 pypi_0 pypi
wheel 0.40.0 pyhd8ed1ab_0 conda-forge
xlrd 1.2.0 pypi_0 pypi
xlwt 1.3.0 pypi_0 pypi
xopen 1.7.0 pypi_0 pypi
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.8.4 h8ee46fc_1 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.3.0 hd590300_0 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 h166bdaf_4 conda-forge
zstd 1.5.2 h3eb15da_6 conda-forge

[zhouyiqi91]

Compared with 1.12.0, the R package vcfR 1.13.0 changed the output format of some files, which caused this problem.
Updating the celescope version to 1.16.0b0 can fix this problem:

pip install celoscope==1.16.0b0

If you don't want to upgrade the version of celescope, you can also lower the vcfR version to 1.12.0.

[jaspitzer]

Hey, thanks for such a rapid response.

After downgrading vcfR to 1.12.0, the problem still persists. Current version shown below:

r-vcfr 1.12.0 r40h8380222_0 conda-forge

The indicated version of celescope is not showing for me.

[zhouyiqi91]

You can see the beta version by using pip install celescope== and the default url(in case you are using mirror and the mirror didn't collect the beta version:

$ pip install -i https://pypi.org/simple celescope== 
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='pypi.org', port=443): Read timed out. (read timeout=15)")': /simple/celescope/
ERROR: Could not find a version that satisfies the requirement celescope== (from versions: 1.1.0, 1.1.1, 1.1.3, 1.1.4, 1.1.6, 1.1.7, 1.1.8b0, 1.1.8, 1.1.9, 1.2.0, 1.3.0, 1.3.1, 1.3.2, 1.4.0, 1.5.0, 1.5.1b0, 1.5.1, 1.5.2, 1.6.0, 1.6.1, 1.7.0, 1.7.1, 1.7.2, 1.8.0, 1.8.1, 1.9.0, 1.10.0, 1.11.0b0, 1.11.0b1, 1.11.0, 1.11.1, 1.12.0b0, 1.12.0, 1.12.1, 1.13.0, 1.14.0b0, 1.14.0, 1.14.1, 1.15.0, 1.15.1, 1.15.2, 1.16.0b0)
ERROR: No matching distribution found for celescope==

And installing 1.16.0b0:

pip install celescope==1.16.0b0 -i https://pypi.org/simple

[zhouyiqi91]

In theory， downgrading vcfR to 1.12.0 should also work. I will take more tests to see why it didn't work.

[zhouyiqi91]

The issue has been fixed in version>1.16.0