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 plotsnp indices = [int(x.split('')[2])-1 for x in variants] File "/home/js/mambaforge/envs/celescope/lib/python3.9/site-packages/celescope/snp/analysissnp.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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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