Hi zumis teams:
Thank you very much for this amazing pipline!
I have generated smart3-seq data and try to use zumis to analysis diff mRNAs and transposons. for mRNAs, it went well. but I have troubles in transposon analysis. the only difference was the gtf I supplied in yaml file. it would be great if you could give me some suggestions!
Using miniconda environment for zUMIs!
note: internal executables will be used instead of those specified in the YAML file!
You provided these parameters:
YAML file: ./project8_TE.yaml
zUMIs directory: /media/nbfs/gongyy/3_smart_seq_rabbit/zUMIs
STAR executable STAR
samtools executable samtools
pigz executable pigz
Rscript executable Rscript
RAM limit: 50
zUMIs version 2.9.7e
Wed Apr 3 10:16:49 CST 2024
WARNING: The STAR version used for mapping is 2.7.3a and the STAR index was created using the ve rsion 2.7.1a. This may lead to an error while mapping. If you encounter any errors at the mappin g stage, please make sure to create the STAR index using STAR 2.7.3a.
Filtering...
Wed Apr 3 10:34:17 CST 2024
[1] " reads were assigned to barcodes that do not correspond to intact cells."
Mapping...
[1] "2024-04-03 10:34:19 CST"
Apr 03 10:34:19 ..... started STAR run
Apr 03 10:34:20 ..... loading genome
Apr 03 10:34:19 ..... started STAR run
Apr 03 10:34:20 ..... loading genome
Apr 03 10:35:44 ..... processing annotations GTF
Apr 03 10:36:10 ..... started mapping
Apr 03 10:36:40 ..... processing annotations GTF
Apr 03 10:37:06 ..... started mapping
Apr 03 10:57:18 ..... finished mapping
Apr 03 10:57:19 ..... finished successfully
Apr 03 11:03:54 ..... finished mapping
Apr 03 11:03:56 ..... finished successfully
Wed Apr 3 11:04:36 CST 2024
Counting...
[1] "2024-04-03 11:04:51 CST"
[1] "7.5e+07 Reads per chunk"
[1] "Loading reference annotation from:"
[1] "/media/nbfs/gongyy/3_smart_seq_rabbit/8_Project_gongyuanyuan_240322N/3_TE_zUMIs/project8_TE .final_annot.gtf"
Error: cannot allocate vector of size 6.6 Gb
In addition: Warning message:
as_quosure() requires an explicit environment as of rlang 0.3.0.
Please supply env.
This warning is displayed once per session.
Execution halted
Warning message:
system call failed: Cannot allocate memory
Wed Apr 3 12:39:59 CST 2024
Loading required package: yaml
Loading required package: Matrix
[1] "loomR found"
Error in gzfile(file, "rb") : cannot open the connection
Calls: rds_to_loom -> readRDS -> gzfile
In addition: Warning message:
In gzfile(file, "rb") :
cannot open compressed file '/media/nbfs/gongyy/3_smart_seq_rabbit/8_Project_gongyuanyuan_2403 22N/3_TE_zUMIs/zUMIs_output/expression/project8_TE.dgecounts.rds', probable reason 'No such file or directory'
Execution halted
Wed Apr 3 12:40:04 CST 2024
Descriptive statistics...
[1] "I am loading useful packages for plotting..."
[1] "2024-04-03 12:40:04 CST"
Error in gzfile(file, "rb") : cannot open the connection
Calls: readRDS -> gzfile
In addition: Warning message:
In gzfile(file, "rb") :
cannot open compressed file '/media/nbfs/gongyy/3_smart_seq_rabbit/8_Project_gongyuanyuan_2403 22N/3_TE_zUMIs/zUMIs_output/expression/project8_TE.dgecounts.rds', probable reason 'No such file or directory'
Execution halted
Wed Apr 3 12:40:12 CST 2024
It looks like the error occurred in the counting step, also the files are missing in expression and stats folder.
Hi zumis teams: Thank you very much for this amazing pipline! I have generated smart3-seq data and try to use zumis to analysis diff mRNAs and transposons. for mRNAs, it went well. but I have troubles in transposon analysis. the only difference was the gtf I supplied in yaml file. it would be great if you could give me some suggestions!
YAML FILE: sequence_files: file1: name: /media/nbfs/gongyy/3_smart_seq_rabbit/8_Project_gongyuanyuan_240322N/1_multiplexed_fastq_files/reads_for_zUMIs.R1.fastq.gz base_definition:
output messages: Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs
Using miniconda environment for zUMIs! note: internal executables will be used instead of those specified in the YAML file!
You provided these parameters: YAML file: ./project8_TE.yaml zUMIs directory: /media/nbfs/gongyy/3_smart_seq_rabbit/zUMIs STAR executable STAR samtools executable samtools pigz executable pigz Rscript executable Rscript RAM limit: 50 zUMIs version 2.9.7e
Wed Apr 3 10:16:49 CST 2024 WARNING: The STAR version used for mapping is 2.7.3a and the STAR index was created using the ve rsion 2.7.1a. This may lead to an error while mapping. If you encounter any errors at the mappin g stage, please make sure to create the STAR index using STAR 2.7.3a. Filtering... Wed Apr 3 10:34:17 CST 2024 [1] " reads were assigned to barcodes that do not correspond to intact cells." Mapping... [1] "2024-04-03 10:34:19 CST" Apr 03 10:34:19 ..... started STAR run Apr 03 10:34:20 ..... loading genome Apr 03 10:34:19 ..... started STAR run Apr 03 10:34:20 ..... loading genome Apr 03 10:35:44 ..... processing annotations GTF Apr 03 10:36:10 ..... started mapping Apr 03 10:36:40 ..... processing annotations GTF Apr 03 10:37:06 ..... started mapping Apr 03 10:57:18 ..... finished mapping Apr 03 10:57:19 ..... finished successfully Apr 03 11:03:54 ..... finished mapping Apr 03 11:03:56 ..... finished successfully Wed Apr 3 11:04:36 CST 2024 Counting... [1] "2024-04-03 11:04:51 CST" [1] "7.5e+07 Reads per chunk" [1] "Loading reference annotation from:" [1] "/media/nbfs/gongyy/3_smart_seq_rabbit/8_Project_gongyuanyuan_240322N/3_TE_zUMIs/project8_TE .final_annot.gtf" Error: cannot allocate vector of size 6.6 Gb In addition: Warning message:
as_quosure()requires an explicit environment as of rlang 0.3.0. Please supplyenv. This warning is displayed once per session. Execution halted Warning message: system call failed: Cannot allocate memory Wed Apr 3 12:39:59 CST 2024 Loading required package: yaml Loading required package: Matrix [1] "loomR found" Error in gzfile(file, "rb") : cannot open the connection Calls: rds_to_loom -> readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/media/nbfs/gongyy/3_smart_seq_rabbit/8_Project_gongyuanyuan_2403 22N/3_TE_zUMIs/zUMIs_output/expression/project8_TE.dgecounts.rds', probable reason 'No such file or directory' Execution halted Wed Apr 3 12:40:04 CST 2024 Descriptive statistics... [1] "I am loading useful packages for plotting..." [1] "2024-04-03 12:40:04 CST" Error in gzfile(file, "rb") : cannot open the connection Calls: readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/media/nbfs/gongyy/3_smart_seq_rabbit/8_Project_gongyuanyuan_2403 22N/3_TE_zUMIs/zUMIs_output/expression/project8_TE.dgecounts.rds', probable reason 'No such file or directory' Execution halted Wed Apr 3 12:40:12 CST 2024It looks like the error occurred in the counting step, also the files are missing in expression and stats folder.
Best Regards, Yuan