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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
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Problems encountered in Smartseq3 data processing #297

Closed zmf0621 closed 2 years ago

zmf0621 commented 2 years ago

Hi Team, congrats on the awesome software! I used zUMIs today for a Smartseq3 data and there was such a problem at first:

[1] "2021-12-06 15:17:51 CST" [1] "Coordinate sorting intermediate bam file..." [bam_sort_core] merging from 0 files and 50 in-memory blocks... [1] "2021-12-06 15:18:22 CST" [1] "Hamming distance collapse in barcode chunk 1 out of 1" Error in mclapply(1:nrow(idxstats), function(x) { : could not find function "mclapply" Calls: reads2genes_new Execution halted Mon Dec 6 15:18:23 CST 2021

I changed the UMIstuffFUN.R file and added ”parallel ::“ at the front Then there is such an error：

[1] "2021-12-06 15:30:39 CST" [1] "Coordinate sorting intermediate bam file..." [bam_sort_core] merging from 0 files and 50 in-memory blocks... [1] "2021-12-06 15:31:38 CST" [1] "Hamming distance collapse in barcode chunk 1 out of 1" Error in rbindlist(rsamtools_reads, fill = TRUE, use.names = TRUE) : Item 1 of input is not a data.frame, data.table or list Calls: reads2genes_new -> rbindlist In addition: Warning message: In parallel::mclapply(1:nrow(idxstats), function(x) { : all scheduled cores encountered errors in user code

####################################### Here is my yaml file： project: B_2_smartseq3 sequence_files: file1: name: /data/lab/Wangjiachen/20211201-0/d1102s3B/B3_1_S1_L003_R1_001.fastq.gz base_definition:

cziegenhain commented 2 years ago

Hi,

If you use the inbuilt conda environment you should get all the packages needed. (just run with zUMIs.sh -c -y myyaml ) Could you post the full verbose from the beginning of the pipeline so I can check what is happening?

Best, Christoph

zmf0621 commented 2 years ago

Thanks for the help! This is a very useful suggestion. I came to the final result after using the inbuilt environment. Although there was a small problem in the STAR part, everything went well with the bam file I got before!

cziegenhain commented 2 years ago

Great! then I will close this issue.

Clarkvale commented 2 years ago

Hi, I am able reproduce this error. I can't use conda directly because I'm working off the Compute Canada servers and conda isn't allowed. So far I've been attempting to use the docker image via Singularity however this solution is definitely non-trivial.

Here's the full output log:

`You provided these parameters: YAML file: /home/clarkb/scratch/burst/ss3/scripts/mouse_cross2.yaml zUMIs directory: /project/6002165/clarkb/zUMIs STAR executable STAR samtools executable /home/clarkb/projects/def-robertf/clarkb/samtools/bin/samtools pigz executable pigz Rscript executable Rscript RAM limit: 90 zUMIs version 2.9.7

Thu Feb 24 06:44:30 PST 2022 WARNING: The STAR version used for mapping is 2.7.9a and the STAR index was created using the version 2.7.4a. This may lead to an error while mapping. If you encounter any errors at the mapping stage, please make sure to create the STAR index using STAR 2.7.9a. Filtering... Thu Feb 24 09:17:54 PST 2022 [1] "396 barcodes detected." [1] "17559218 reads were assigned to barcodes that do not correspond to intact cells." [1] "Found 14769 daughter barcodes that can be binned into 389 parent barcodes." [1] "Binned barcodes correspond to 17487434 reads." Mapping... [1] "2022-02-24 09:34:49 PST" STAR --readFilesCommand /home/clarkb/projects/def-robertf/clarkb/samtools/bin/samtools view -@ 2 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --genomeDir /home/clarkb/scratch/star_index/n_masked_GRCm38.68_CAST --sjdbGTFfile /home/clarkb/scratch/star_index/mm10/Mus_musculus.GRCm38.68.gtf --runThreadN 6 --sjdbOverhang 149 --readFilesType SAM PE --limitSjdbInsertNsj 2000000 --clip3pAdapterMMp 0.1 0.1 --clip3pAdapterSeq CTGTCTCTTATACACATCT CTGTCTCTTATACACATCT --readFilesIn /home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsah.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsai.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsaj.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsak.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsal.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsam.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsan.filtered.tagged.bam --outFileNamePrefix /home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMap//tmp.Smartseq3_Fibroblasts.2. STAR version: 2.7.9a compiled: 2021-07-08T15:06:22+00:00 build-node.computecanada.ca:/tmp/ebuser/avx2/STAR/2.7.9a/GCCcore-9.3.0/STAR-2.7.9a/source Feb 24 09:34:51 ..... started STAR run Feb 24 09:34:52 ..... loading genome STAR --readFilesCommand /home/clarkb/projects/def-robertf/clarkb/samtools/bin/samtools view -@ 2 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --genomeDir /home/clarkb/scratch/star_index/n_masked_GRCm38.68_CAST --sjdbGTFfile /home/clarkb/scratch/star_index/mm10/Mus_musculus.GRCm38.68.gtf --runThreadN 6 --sjdbOverhang 149 --readFilesType SAM PE --limitSjdbInsertNsj 2000000 --clip3pAdapterMMp 0.1 0.1 --clip3pAdapterSeq CTGTCTCTTATACACATCT CTGTCTCTTATACACATCT --readFilesIn /home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsaa.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsab.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsac.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsad.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsae.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsaf.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsag.filtered.tagged.bam --outFileNamePrefix /home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMap//tmp.Smartseq3_Fibroblasts.1. STAR version: 2.7.9a compiled: 2021-07-08T15:06:22+00:00 build-node.computecanada.ca:/tmp/ebuser/avx2/STAR/2.7.9a/GCCcore-9.3.0/STAR-2.7.9a/source Feb 24 09:34:51 ..... started STAR run Feb 24 09:34:53 ..... loading genome STAR --readFilesCommand /home/clarkb/projects/def-robertf/clarkb/samtools/bin/samtools view -@ 2 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --genomeDir /home/clarkb/scratch/star_index/n_masked_GRCm38.68_CAST --sjdbGTFfile /home/clarkb/scratch/star_index/mm10/Mus_musculus.GRCm38.68.gtf --runThreadN 6 --sjdbOverhang 149 --readFilesType SAM PE --limitSjdbInsertNsj 2000000 --clip3pAdapterMMp 0.1 0.1 --clip3pAdapterSeq CTGTCTCTTATACACATCT CTGTCTCTTATACACATCT --readFilesIn /home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsao.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsap.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsaq.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsar.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsas.filtered.tagged.bam,/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMerge//Smartseq3_Fibroblasts.Smartseq3_Fibroblastsat.filtered.tagged.bam --outFileNamePrefix /home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/.tmpMap//tmp.Smartseq3_Fibroblasts.3. STAR version: 2.7.9a compiled: 2021-07-08T15:06:22+00:00 build-node.computecanada.ca:/tmp/ebuser/avx2/STAR/2.7.9a/GCCcore-9.3.0/STAR-2.7.9a/source Feb 24 09:34:51 ..... started STAR run Feb 24 09:34:53 ..... loading genome Feb 24 09:36:07 ..... processing annotations GTF Feb 24 09:36:07 ..... processing annotations GTF Feb 24 09:36:07 ..... processing annotations GTF Feb 24 09:36:17 ..... inserting junctions into the genome indices Feb 24 09:36:17 ..... inserting junctions into the genome indices Feb 24 09:36:17 ..... inserting junctions into the genome indices Feb 24 09:38:20 ..... started mapping Feb 24 09:38:22 ..... started mapping Feb 24 09:38:26 ..... started mapping Feb 24 12:21:33 ..... finished mapping Feb 24 12:21:37 ..... finished successfully Feb 24 12:48:15 ..... finished mapping Feb 24 12:48:19 ..... finished successfully Feb 24 12:58:48 ..... finished mapping Feb 24 12:58:54 ..... finished successfully Thu Feb 24 13:08:24 PST 2022 Counting... [1] "2022-02-24 13:08:52 PST" [1] "1.35e+08 Reads per chunk" [1] "Loading reference annotation from:" [1] "/home/clarkb/scratch/burst/ss3/zUMI_out/Smartseq3_Fibroblasts.final_annot.gtf" [1] "Annotation loaded!" [1] "Assigning reads to features (ex)"

    ==========     _____ _    _ ____  _____  ______          _____
    =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
      =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
        ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
          ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
    ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
   Rsubread 1.32.4
//========================== featureCounts setting ===========================\ Input files : 1 BAM file P Smartseq3_Fibroblasts.filtered.tagged.Alig ...
Annotation : R data.frame
Assignment details : .featureCounts.bam
(Note that files are saved to the output directory)
Dir for temp files : .
Threads : 20
Level : meta-feature level
Paired-end : yes
Multimapping reads : counted
Multiple alignments : primary alignment only
Multi-overlapping reads : not counted
Min overlapping bases : 1
Chimeric reads : not counted
Both ends mapped : not required

\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\ Load annotation file .Rsubread_UserProvidedAnnotation_pid9444 ... Features : 244055 Meta-features : 37315 Chromosomes/contigs : 43
Process BAM file Smartseq3_Fibroblasts.filtered.tagged.Aligned.out.bam...
Paired-end reads are included.
Assign alignments (paired-end) to features...
WARNING: reads from the same pair were found not adjacent to each
other in the input (due to read sorting by location or
reporting of multi-mapping read pairs).
Pairing up the read pairs.
Total alignments : 569248844
Successfully assigned alignments : 454299881 (79.8%)
Running time : 12.65 minutes

\===================== http://subread.sourceforge.net/ ======================//

[1] "Assigning reads to features (in)"

    ==========     _____ _    _ ____  _____  ______          _____
    =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
      =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
        ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
          ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
    ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
   Rsubread 1.32.4
//========================== featureCounts setting ===========================\ Input files : 1 BAM file P Smartseq3_Fibroblasts.filtered.tagged.Alig ...
Annotation : R data.frame
Assignment details : .featureCounts.bam
(Note that files are saved to the output directory)
Dir for temp files : .
Threads : 20
Level : meta-feature level
Paired-end : yes
Multimapping reads : counted
Multiple alignments : primary alignment only
Multi-overlapping reads : not counted
Min overlapping bases : 1
Chimeric reads : not counted
Both ends mapped : not required

\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\ Load annotation file .Rsubread_UserProvidedAnnotation_pid9444 ... Features : 196191 Meta-features : 21690 Chromosomes/contigs : 38
Process BAM file Smartseq3_Fibroblasts.filtered.tagged.Aligned.out.bam ...
Paired-end reads are included.
Assign alignments (paired-end) to features...
WARNING: reads from the same pair were found not adjacent to each
other in the input (due to read sorting by location or
reporting of multi-mapping read pairs).
Pairing up the read pairs.
WARNING: reads from the same pair were found not adjacent to each
other in the input (due to read sorting by location or
reporting of multi-mapping read pairs).
Pairing up the read pairs.
Total alignments : 569248844
Successfully assigned alignments : 44806224 (7.9%)
Running time : 12.73 minutes

\===================== http://subread.sourceforge.net/ ======================//

[1] "2022-02-24 13:35:15 PST" [1] "Coordinate sorting intermediate bam file..." [bam_sort_core] merging from 120 files and 20 in-memory blocks... [1] "2022-02-24 15:44:59 PST" [1] "Hamming distance collapse in barcode chunk 1 out of 5" Error in rbindlist(rsamtools_reads, fill = TRUE, use.names = TRUE) : Item 1 of input is not a data.frame, data.table or list Calls: reads2genes_new -> rbindlist In addition: Warning message: In parallel::mclapply(1:nrow(idxstats), function(x) { : all scheduled cores encountered errors in user code Execution halted Thu Feb 24 15:45:01 PST 2022 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 '/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/expression/Smartseq3_Fibroblasts.dgecounts.rds', probable reason 'No such file or directory' Execution halted Thu Feb 24 15:45:09 PST 2022 Descriptive statistics... [1] "I am loading useful packages for plotting..." [1] "2022-02-24 15:45:10 PST" Error in gzfile(file, "rb") : cannot open the connection Calls: readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/home/clarkb/scratch/burst/ss3/zUMI_out/zUMIs_output/expression/Smartseq3_Fibroblasts.dgecounts.rds', probable reason 'No such file or directory' Execution halted Thu Feb 24 15:45:36 PST 2022`

And here is the yaml file:

project: Smartseq3_Fibroblasts sequence_files: file1: name: /home/clarkb/scratch/burst/ss3/reads/Smartseq3.Fibroblasts.NovaSeq.R1.fastq.gz base_definition:

Any help would be super appreciated.

ROund-code commented 2 years ago

Hi, Have you fixed that problem? when I run example data, I also produced that error message. Here's the full output log: Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs

You provided these parameters: YAML file: runExample.yaml zUMIs directory: /media/nbfs/gongyy/3_smart_seq_rabbit/3_zUMIs STAR executable /home/novelbio/miniconda2/bin/STAR samtools executable /usr/bin/samtools pigz executable /usr/bin/pigz Rscript executable /usr/bin/Rscript RAM limit: 40 zUMIs version 2.9.7

Thu May 5 15:42:15 CST 2022 Filtering... Thu May 5 15:42:32 CST 2022 [1] "43 barcodes detected." [1] "193783 reads were assigned to barcodes that do not correspond to intact cells." Mapping... [1] "2022-05-05 15:42:37 CST" Warning message: NAs introduced by coercion May 05 15:42:38 ..... started STAR run May 05 15:42:38 ..... loading genome May 05 15:42:39 ..... processing annotations GTF May 05 15:42:39 ..... inserting junctions into the genome indices May 05 15:42:45 ..... started mapping May 05 15:45:22 ..... finished mapping May 05 15:45:23 ..... finished successfully Thu May 5 15:45:23 CST 2022 Counting... [1] "2022-05-05 15:45:42 CST" [1] "1.8e+08 Reads per chunk" [1] "Loading reference annotation from:" [1] "/media/nbfs/gongyy/3_smart_seq_rabbit/0_example/output/Example.final_annot.gtf" [1] "Annotation loaded!" [1] "Assigning reads to features (ex)"

    ==========     _____ _    _ ____  _____  ______          _____
    =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
      =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
        ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
          ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
    ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
   Rsubread 1.32.4
//========================== featureCounts setting ===========================\ Input files : 1 BAM file S Example.filtered.tagged.Aligned.out.bam
Annotation : R data.frame
Assignment details : .featureCounts.bam
(Note that files are saved to the output directory)
Dir for temp files : .
Threads : 8
Level : meta-feature level
Paired-end : yes
Multimapping reads : counted
Multiple alignments : primary alignment only
Multi-overlapping reads : not counted
Min overlapping bases : 1
Chimeric reads : not counted
Both ends mapped : not required

\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\ Load annotation file .Rsubread_UserProvidedAnnotation_pid10627 ... Features : 7370 Meta-features : 1353 Chromosomes/contigs : 1
Process BAM file Example.filtered.tagged.Aligned.out.bam...
Single-end reads are included.
Assign alignments to features...
Total alignments : 853296
Successfully assigned alignments : 20901 (2.4%)
Running time : 0.03 minutes

\===================== http://subread.sourceforge.net/ ======================//

[1] "Assigning reads to features (in)"

    ==========     _____ _    _ ____  _____  ______          _____
    =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
      =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
        ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
          ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
    ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
   Rsubread 1.32.4
//========================== featureCounts setting ===========================\ Input files : 1 BAM file S Example.filtered.tagged.Aligned.out.bam.ex ...
Annotation : R data.frame
Assignment details : .featureCounts.bam
(Note that files are saved to the output directory)
Dir for temp files : .
Threads : 8
Level : meta-feature level
Paired-end : yes
Multimapping reads : counted
Multiple alignments : primary alignment only
Multi-overlapping reads : not counted
Min overlapping bases : 1
Chimeric reads : not counted
Both ends mapped : not required

\===================== http://subread.sourceforge.net/ ======================//

//================================= Running ==================================\ Load annotation file .Rsubread_UserProvidedAnnotation_pid10627 ... Features : 4843 Meta-features : 677 Chromosomes/contigs : 1
Process BAM file Example.filtered.tagged.Aligned.out.bam.ex.featureCou ...
Single-end reads are included.
Assign alignments to features...
Total alignments : 853296
Successfully assigned alignments : 43386 (5.1%)
Running time : 0.03 minutes

\===================== http://subread.sourceforge.net/ ======================//

[1] "2022-05-05 15:46:03 CST" [1] "Coordinate sorting final bam file..." [bam_sort_core] merging from 0 files and 8 in-memory blocks... [1] "2022-05-05 15:46:06 CST" [1] "Here are the detected subsampling options:" [1] "Automatic downsampling" [1] "Working on barcode chunk 1 out of 1" [1] "Processing 43 barcodes in this chunk..." Error in mclapply(1:nrow(idxstats), function(x) { : could not find function "mclapply" Calls: reads2genes_new Execution halted Thu May 5 15:46:07 CST 2022 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/0_example/output/zUMIs_output/expression/Example.dgecounts.rds', probable reason 'No such file or directory' Execution halted Thu May 5 15:46:12 CST 2022 Descriptive statistics... [1] "I am loading useful packages for plotting..." [1] "2022-05-05 15:46:12 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/0_example/output/zUMIs_output/expression/Example.dgecounts.rds', probable reason 'No such file or directory' Execution halted Thu May 5 15:46:25 CST 2022

cziegenhain commented 2 years ago

Hi,

I have found that this is caused by a change in RSamtools which is one of the dependencies used. Hopefully I find the time to push the fix later today - in the meantime the inbuilt conda environment remains as an option with the functional combination of versions of all dependencies.

Best, Christoph

ROund-code commented 2 years ago

Hi,

Thanks for your help and prompt reply, I will try to use the inbuilt conda environment as you suggested, will let you know the results. also it will be great if you could fix that RSamtools problems!

Best Regards, Yvonne

Clarkvale commented 2 years ago

I resolved the problem by using TomKellyGenetics' branch with some of my own minor fixes. The problem seem to be parsing '*' symbols in bamfiles. I also had to the parallel package to the namespace in the functions R script. My fork is here: https://github.com/Clarkvale/zUMIs

cziegenhain commented 2 years ago

I pushed the fix for the change in Rsamtools behavior earlier today.

ROund-code commented 2 years ago

Hi cziegenhain and clarkvale:

The updated version works well for me, thank you for your generous help.

Best Regards, Yvonne