Comments (10)
SoberDog
commented on June 24, 2024
I install R and the R-packages by conda.
And the full log is show in below
##############################################################
# SCASA V1.0.1
# SINGLE CELL TRANSCRIPT QUANTIFICATION TOOL
# Version Date: 2022-03-24
# FOR ANY ISSUES, CONTACT: [email protected]
# https://github.com/eudoraleer/scasa/
##############################################################
Directory ./ already exists. Writing into existing directory..
mkdir: cannot create directory ‘.//SCASA_My_Project_20221014093239/’: File exists
Preparing for alignment..
Indexing reference..
Directory .//SCASA_My_Project_20221014093239/0PRESETS//REF_INDEX/ already exists. Writing into existing directory..
Version Info: ### PLEASE UPGRADE SALMON ###
### A newer version of salmon with important bug fixes and improvements is available. ####
###
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.
###
Sign up for the salmon mailing list to hear about new versions, features and updates at:
https://oceangenomics.com/subscribe
###[2022-10-14 09:32:40.162] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.
[2022-10-14 09:32:40.162] [jLog] [info] building index
out : .//SCASA_My_Project_20221014093239/0PRESETS//REF_INDEX/
[2022-10-14 09:32:40.181] [puff::index::jointLog] [info] Running fixFasta
[Step 1 of 4] : counting k-mers
[2022-10-14 09:32:44.999] [puff::index::jointLog] [warning] Removed 236 transcripts that were sequence duplicates of indexed transcripts.
[2022-10-14 09:32:44.999] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2022-10-14 09:32:44.999] [puff::index::jointLog] [info] Replaced 4 non-ATCG nucleotides
[2022-10-14 09:32:44.999] [puff::index::jointLog] [info] Clipped poly-A tails from 11,186 transcripts
wrote 76267 cleaned references
[2022-10-14 09:32:45.302] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-10-14 09:32:47.287] [puff::index::jointLog] [info] ntHll estimated 85097693 distinct k-mers, setting filter size to 2^31
Threads = 2
Vertex length = 31
Hash functions = 5
Filter size = 2147483648
Capacity = 2
Files:
.//SCASA_My_Project_20221014093239/0PRESETS//REF_INDEX/ref_k31_fixed.fa
--------------------------------------------------------------------------------
Round 0, 0:2147483648
Pass Filling Filtering
1 24 56
2 4 0
True junctions count = 277411
False junctions count = 439286
Hash table size = 716697
Candidate marks count = 4699425
--------------------------------------------------------------------------------
Reallocating bifurcations time: 0
True marks count: 3337299
Edges construction time: 3
--------------------------------------------------------------------------------
Distinct junctions = 277411
allowedIn: 12
Max Junction ID: 318881
seen.size():2551057 kmerInfo.size():318882
approximateContigTotalLength: 66002535
counters for complex kmers:
(prec>1 & succ>1)=26025 | (succ>1 & isStart)=69 | (prec>1 & isEnd)=67 | (isStart & isEnd)=10
contig count: 433949 element count: 98078572 complex nodes: 26171
# of ones in rank vector: 433948
[2022-10-14 09:34:23.329] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-10-14 09:34:23.329] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory .//SCASA_My_Project_20221014093239/0PRESETS//REF_INDEX
size = 98078572
-----------------------------------------
| Loading contigs | Time = 5.2253 ms
-----------------------------------------
size = 98078572
-----------------------------------------
| Loading contig boundaries | Time = 2.9247 ms
-----------------------------------------
Number of ones: 433948
Number of ones per inventory item: 512
Inventory entries filled: 848
433948
[2022-10-14 09:34:23.457] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-10-14 09:34:23.459] [puff::index::jointLog] [info] contig count for validation: 433,948
[2022-10-14 09:34:23.575] [puff::index::jointLog] [info] Total # of Contigs : 433,948
[2022-10-14 09:34:23.575] [puff::index::jointLog] [info] Total # of numerical Contigs : 433,948
[2022-10-14 09:34:23.593] [puff::index::jointLog] [info] Total # of contig vec entries: 3,427,302
[2022-10-14 09:34:23.593] [puff::index::jointLog] [info] bits per offset entry 22
[2022-10-14 09:34:23.640] [puff::index::jointLog] [info] Done constructing the contig vector. 433949
[2022-10-14 09:34:23.727] [puff::index::jointLog] [info] # segments = 433,948
[2022-10-14 09:34:23.727] [puff::index::jointLog] [info] total length = 98,078,572
[2022-10-14 09:34:23.742] [puff::index::jointLog] [info] Reading the reference files ...
[2022-10-14 09:34:24.195] [puff::index::jointLog] [info] positional integer width = 27
[2022-10-14 09:34:24.195] [puff::index::jointLog] [info] seqSize = 98,078,572
[2022-10-14 09:34:24.195] [puff::index::jointLog] [info] rankSize = 98,078,572
[2022-10-14 09:34:24.195] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-10-14 09:34:24.195] [puff::index::jointLog] [info] num keys = 85,060,132
for info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000
[Building BooPHF] 99.9 % elapsed: 0 min 6 sec remaining: 0 min 0 sec
Bitarray 445693632 bits (100.00 %) (array + ranks )
final hash 0 bits (0.00 %) (nb in final hash 0)
[2022-10-14 09:34:29.716] [puff::index::jointLog] [info] mphf size = 53.1308 MB
[2022-10-14 09:34:29.743] [puff::index::jointLog] [info] chunk size = 49,039,286
[2022-10-14 09:34:29.743] [puff::index::jointLog] [info] chunk 0 = [0, 49,039,286)
[2022-10-14 09:34:29.743] [puff::index::jointLog] [info] chunk 1 = [49,039,286, 98,078,542)
[2022-10-14 09:34:38.224] [puff::index::jointLog] [info] finished populating pos vector
[2022-10-14 09:34:38.224] [puff::index::jointLog] [info] writing index components
[2022-10-14 09:34:38.357] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-10-14 09:34:38.384] [jLog] [info] done building index
Finnished indexing reference..
Begins pseudo-alignment..
nohup: redirecting stderr to stdout
Congratulations! Pseudo-alignment has completed in 30 seconds!
Scasa quantification has started..
Begin Scasa quantification for sample Sample_01_S1_L001..
Error in file(con, "r") : cannot open the connection
Calls: readLines -> file
In addition: Warning message:
In file(con, "r") :
cannot open file './/SCASA_My_Project_20221014093239/1ALIGN//Sample_01_S1_L001_alignout/alevin/bfh.txt': No such file or directory
Execution halted
Loading required package: iterators
Loading required package: parallel
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file '/storage/data/GYD/Softwares/scasa/Test_Dataset/SCASA_My_Project_20221014093239/2QUANT/Sample_01_S1_L001_quant/Sample_eqClass.RData', probable reason 'No such file or directory'
Execution halted
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file './/SCASA_My_Project_20221014093239/2QUANT//Sample_01_S1_L001_quant//scasa_isoform_expression.RData', probable reason 'No such file or directory'
Execution halted
Congratulations! Scasa single cell RNA-Seq transcript quantification has completed in 30 seconds!
All done!from scasa.
nghiavtr
commented on June 24, 2024
Hi @SoberDog,
Thank you for using Scasa. Your alevin.log indicates that there is a conflict between the cDNA file and the transcript-gene mapping file (https://github.com/eudoraleer/scasa/blob/main/scasa/REFERENCE/txp2gene_hg38.tsv). I guess you might download the latest version of hg38 which has some small differences from the older one.
So, the simple solution is using the cDNA fasta version we suggested (downloaded here https://www.dropbox.com/s/xoa6yl562a5lv35/refMrna.fa.gz)
If you really need to use the latest version, then it requires preparing a new txp2gene_hg38.tsv file and follow the instruction in (https://github.com/eudoraleer/scasa/wiki) to generate a proper X-matrix for replacement in scasa/REFERENCE folder.
Best,
Nghia
from scasa.
ThepeachYolado
commented on June 24, 2024
I install R and the R-packages by conda. And the full log is show in below
############################################################## # SCASA V1.0.1 # SINGLE CELL TRANSCRIPT QUANTIFICATION TOOL # Version Date: 2022-03-24 # FOR ANY ISSUES, CONTACT: [email protected] # https://github.com/eudoraleer/scasa/ ############################################################## Directory ./ already exists. Writing into existing directory.. mkdir: cannot create directory ‘.//SCASA_My_Project_20221014093239/’: File exists Preparing for alignment.. Indexing reference.. Directory .//SCASA_My_Project_20221014093239/0PRESETS//REF_INDEX/ already exists. Writing into existing directory.. Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### Sign up for the salmon mailing list to hear about new versions, features and updates at: https://oceangenomics.com/subscribe ###[2022-10-14 09:32:40.162] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode. [2022-10-14 09:32:40.162] [jLog] [info] building index out : .//SCASA_My_Project_20221014093239/0PRESETS//REF_INDEX/ [2022-10-14 09:32:40.181] [puff::index::jointLog] [info] Running fixFasta [Step 1 of 4] : counting k-mers [2022-10-14 09:32:44.999] [puff::index::jointLog] [warning] Removed 236 transcripts that were sequence duplicates of indexed transcripts. [2022-10-14 09:32:44.999] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag [2022-10-14 09:32:44.999] [puff::index::jointLog] [info] Replaced 4 non-ATCG nucleotides [2022-10-14 09:32:44.999] [puff::index::jointLog] [info] Clipped poly-A tails from 11,186 transcripts wrote 76267 cleaned references [2022-10-14 09:32:45.302] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers [2022-10-14 09:32:47.287] [puff::index::jointLog] [info] ntHll estimated 85097693 distinct k-mers, setting filter size to 2^31 Threads = 2 Vertex length = 31 Hash functions = 5 Filter size = 2147483648 Capacity = 2 Files: .//SCASA_My_Project_20221014093239/0PRESETS//REF_INDEX/ref_k31_fixed.fa -------------------------------------------------------------------------------- Round 0, 0:2147483648 Pass Filling Filtering 1 24 56 2 4 0 True junctions count = 277411 False junctions count = 439286 Hash table size = 716697 Candidate marks count = 4699425 -------------------------------------------------------------------------------- Reallocating bifurcations time: 0 True marks count: 3337299 Edges construction time: 3 -------------------------------------------------------------------------------- Distinct junctions = 277411 allowedIn: 12 Max Junction ID: 318881 seen.size():2551057 kmerInfo.size():318882 approximateContigTotalLength: 66002535 counters for complex kmers: (prec>1 & succ>1)=26025 | (succ>1 & isStart)=69 | (prec>1 & isEnd)=67 | (isStart & isEnd)=10 contig count: 433949 element count: 98078572 complex nodes: 26171 # of ones in rank vector: 433948 [2022-10-14 09:34:23.329] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file. [2022-10-14 09:34:23.329] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory .//SCASA_My_Project_20221014093239/0PRESETS//REF_INDEX size = 98078572 ----------------------------------------- | Loading contigs | Time = 5.2253 ms ----------------------------------------- size = 98078572 ----------------------------------------- | Loading contig boundaries | Time = 2.9247 ms ----------------------------------------- Number of ones: 433948 Number of ones per inventory item: 512 Inventory entries filled: 848 433948 [2022-10-14 09:34:23.457] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure. [2022-10-14 09:34:23.459] [puff::index::jointLog] [info] contig count for validation: 433,948 [2022-10-14 09:34:23.575] [puff::index::jointLog] [info] Total # of Contigs : 433,948 [2022-10-14 09:34:23.575] [puff::index::jointLog] [info] Total # of numerical Contigs : 433,948 [2022-10-14 09:34:23.593] [puff::index::jointLog] [info] Total # of contig vec entries: 3,427,302 [2022-10-14 09:34:23.593] [puff::index::jointLog] [info] bits per offset entry 22 [2022-10-14 09:34:23.640] [puff::index::jointLog] [info] Done constructing the contig vector. 433949 [2022-10-14 09:34:23.727] [puff::index::jointLog] [info] # segments = 433,948 [2022-10-14 09:34:23.727] [puff::index::jointLog] [info] total length = 98,078,572 [2022-10-14 09:34:23.742] [puff::index::jointLog] [info] Reading the reference files ... [2022-10-14 09:34:24.195] [puff::index::jointLog] [info] positional integer width = 27 [2022-10-14 09:34:24.195] [puff::index::jointLog] [info] seqSize = 98,078,572 [2022-10-14 09:34:24.195] [puff::index::jointLog] [info] rankSize = 98,078,572 [2022-10-14 09:34:24.195] [puff::index::jointLog] [info] edgeVecSize = 0 [2022-10-14 09:34:24.195] [puff::index::jointLog] [info] num keys = 85,060,132 for info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 [Building BooPHF] 99.9 % elapsed: 0 min 6 sec remaining: 0 min 0 sec Bitarray 445693632 bits (100.00 %) (array + ranks ) final hash 0 bits (0.00 %) (nb in final hash 0) [2022-10-14 09:34:29.716] [puff::index::jointLog] [info] mphf size = 53.1308 MB [2022-10-14 09:34:29.743] [puff::index::jointLog] [info] chunk size = 49,039,286 [2022-10-14 09:34:29.743] [puff::index::jointLog] [info] chunk 0 = [0, 49,039,286) [2022-10-14 09:34:29.743] [puff::index::jointLog] [info] chunk 1 = [49,039,286, 98,078,542) [2022-10-14 09:34:38.224] [puff::index::jointLog] [info] finished populating pos vector [2022-10-14 09:34:38.224] [puff::index::jointLog] [info] writing index components [2022-10-14 09:34:38.357] [puff::index::jointLog] [info] finished writing dense pufferfish index [2022-10-14 09:34:38.384] [jLog] [info] done building index Finnished indexing reference.. Begins pseudo-alignment.. nohup: redirecting stderr to stdout Congratulations! Pseudo-alignment has completed in 30 seconds! Scasa quantification has started.. Begin Scasa quantification for sample Sample_01_S1_L001.. Error in file(con, "r") : cannot open the connection Calls: readLines -> file In addition: Warning message: In file(con, "r") : cannot open file './/SCASA_My_Project_20221014093239/1ALIGN//Sample_01_S1_L001_alignout/alevin/bfh.txt': No such file or directory Execution halted Loading required package: iterators Loading required package: parallel Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection Calls: load -> readChar In addition: Warning message: In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file '/storage/data/GYD/Softwares/scasa/Test_Dataset/SCASA_My_Project_20221014093239/2QUANT/Sample_01_S1_L001_quant/Sample_eqClass.RData', probable reason 'No such file or directory' Execution halted Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection Calls: load -> readChar In addition: Warning message: In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file './/SCASA_My_Project_20221014093239/2QUANT//Sample_01_S1_L001_quant//scasa_isoform_expression.RData', probable reason 'No such file or directory' Execution halted Congratulations! Scasa single cell RNA-Seq transcript quantification has completed in 30 seconds! All done!
Did you solve it? I had the same problem. Thanks!
from scasa.
nghiavtr
commented on June 24, 2024
Hi @yangwh1998 @SoberDog,
It is likely the issues you guys got were caused by not correct settings or running environment. For convenient, we have a built a docker for scasa which an instruction of how to use for the example data here: https://github.com/eudoraleer/scasa/blob/main/README.md#using-docker-to-run-scasa
Using docker, you don't have to install R packages, salmon, scasa separately. Users just need to revise the setting and input in docker_params.sh. I hope it would make scasa easier to use.
Best,
Nghia
from scasa.
SoberDog
commented on June 24, 2024
Hi, @nghiavtr,
Thanks for deploying the docker, I will try.
Best Regards,
Soberdog
from scasa.
oucstar
commented on June 24, 2024
@nghiavtr , Sorry to bother you, but I have encountered a problem when running your software, which has not been solved, When I set up a new X-matrix for my species annotation file, When I run Rscript $scasaPath/../aux/gen_tx2gene.R cdna=$refFile gtf=$gtfFile sqlite=$sqliteFile cdnaout=$refCleanFile out=$txp2geneFile,It is always making mistakes:
not in gtf: 87794Error in S4Vectors:::normarg_names(value, class(x), length(x)) :
attempt to set too many names (1) on GroupedIRanges object of length 0
Calls: names<- -> names<- -> names<- -> names<- ->
This is my gtf file:
lg3 transdecoder gene 18426480 18430230 . + . gene_id "PB.10003";
lg3 transdecoder transcript 18426480 18429150 . + . transcript_id "PB.10003.6.p1"; gene_id "PB.10003";
lg3 transdecoder exon 18426480 18426570 . + . transcript_id "PB.10003.6.p1"; gene_id "PB.10003";
lg3 transdecoder CDS 18426482 18426570 . + 0 transcript_id "PB.10003.6.p1"; gene_id "PB.10003";
lg3 transdecoder exon 18426689 18426803 . + . transcript_id "PB.10003.6.p1"; gene_id "PB.10003";
lg3 transdecoder CDS 18426689 18426803 . + 1 transcript_id "PB.10003.6.p1"; gene_id "PB.10003";
lg3 transdecoder exon 18427439 18427627 . + . transcript_id "PB.10003.6.p1"; gene_id "PB.10003";
lg3 transdecoder CDS 18427439 18427627 . + 0 transcript_id "PB.10003.6.p1"; gene_id "PB.10003";
lg3 transdecoder exon 18428648 18429150 . + . transcript_id "PB.10003.6.p1"; gene_id "PB.10003";
lg3 transdecoder CDS 18428648 18428749 . + 0 transcript_id "PB.10003.6.p1"; gene_id "PB.10003";
lg3 transdecoder three_prime_UTR 18428750 18429150 . + . transcript_id "PB.10003.6.p1"; gene_id "PB.10003";
lg3 transdecoder transcript 18426689 18430230 . + . transcript_id "PB.10003.7.p1"; gene_id "PB.10003";
lg3 transdecoder exon 18426689 18426803 . + . transcript_id "PB.10003.7.p1"; gene_id "PB.10003";
lg3 transdecoder CDS 18426690 18426803 . + 0 transcript_id "PB.10003.7.p1"; gene_id "PB.10003";
lg3 transdecoder exon 18427439 18427627 . + . transcript_id "PB.10003.7.p1"; gene_id "PB.10003";
lg3 transdecoder CDS 18427439 18427627 . + 0 transcript_id "PB.10003.7.p1"; gene_id "PB.10003";
lg3 transdecoder exon 18428648 18430230 . + . transcript_id "PB.10003.7.p1"; gene_id "PB.10003";
lg3 transdecoder CDS 18428648 18428749 . + 0 transcript_id "PB.10003.7.p1"; gene_id "PB.10003";
lg3 transdecoder three_prime_UTR 18428750 18430230 . + . transcript_id "PB.10003.7.p1"; gene_id "PB.10003";
Could you take a look at it for me? I'd appreciate it if you could help!
from scasa.
nghiavtr
commented on June 24, 2024
Hi @oucstar ,
It looks like that some transcripts in the cdna file are not found in the gtf file. Can you send me both cdna fasta and gtf files (via email to [email protected]), that I can have a look closer?
Nghia
from scasa.
oucstar
commented on June 24, 2024
@nghiavtr ,Sorry to bother you, but is it me you are @?
from scasa.
nghiavtr
commented on June 24, 2024
@nghiavtr ,Sorry to bother you, but is it me you are @?
Yes, @oucstar , sorry I referred to a wrong person. Just send me your file I will have a check.
Nghia
from scasa.
oucstar
commented on June 24, 2024
@nghiavtr ,Ok, I will send it to you after sorting it out. Thank you for your warm reply!
from scasa.
Related Issues (11)
- mkdir errors HOT 3
- Using your tool for single cell data barcoded with split-seq technology and not droplet based HOT 1
- fail in docker: Total 0 white-listed Barcodes HOT 9
- Quantification Fails HOT 3
- QOL change: reset command line color changed by die commands in perl script
- Symlink to binary not supported but no error provided
- Scasa:v1.0.1 docker shows error HOT 3
- no mapped reads in test on SRA sample HOT 1
- So many Error messages: please help HOT 13
- Smart-seq2 full length RNA-seq data HOT 1
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from scasa.