jumphone / sprint Goto Github PK

Hi,

I am trying to use the binaries but they report the following error:

$ sprint
zsh: exec format error: sprint

Can you please help?

Hi,
I found there are files: regular_alu.res, regular_nalurp.res, regular_nrp.res, regular_split.res, regular_overall.res.
Could I use them to count the RNA editing sites in Alu, non-Alu and non-repeat region?

Thanks.

I have mapped identified RES with the referance genome . now i wanna find and count the no. of editing site present in UTR or CDS region ???
` head SPRINT_identified_all.res.col3.sorted.results.mapped.bed

`1A 124189778 124189779|1A 124189772 124190156 TraesCS1A02G117000.1 0 -
1A 124189787 124189788|1A 124189772 124190156 TraesCS1A02G117000.1 0 -
1A 124189792 124189793|1A 124189772 124190156 TraesCS1A02G117000.1 0 -
1A 124189797 124189798|1A 124189772 124190156 TraesCS1A02G117000.1 0 -
1A 124787186 124787187|1A 124786601 124787399 TraesCS1A02G117400.1 0 -
1A 124787192 124787193|1A 124786601 124787399 TraesCS1A02G117400.1 0 -
1A 124787204 124787205|1A 124786601 124787399 TraesCS1A02G117400.1 0 -
1A 124787218 124787219|1A 124786601 124787399 TraesCS1A02G117400.1 0 -
1A 124787237 124787238|1A 124786601 124787399 TraesCS1A02G117400.1 0 -
1A 225507600 225507601|1A 225507557 225517408 TraesCS1A02G137900.1 0 -

Hi @jumphone

Great tool!

I have reverse stranded 100bp paired end RNAseq and I specified -ss 1 assuming reverse == sense strandedness. However, in the output I see that the vast majority of AG editing types are on the - strand, and TC on the + strand which is opposite of what i expected.

I ran sprint from fastq on trimmed unzipped fastqs with command

sprint main -rp hg38_repeat.txt -ss 1 -p 12 -1 sample_1_R1.fq -2 sample_1_R2.fq GRCh38.dna.primary_assembly.fa $OUT/sample_1 bwa samtools

Can you confirm that i should specify -ss 1 for reverse stranded RNAseq?

Thanks very much!
Oliver

http://sprint.tianlab.cn/SPRINT/dbrep/ is not available !

I am trying to look at RNA editing sites for multiple samples. I successfully ran sprint prepare, changed my repeat masker to bed file, etc. but with main - it runs and hits an error but it does not terminate the program. Using bwa0.7.17 and samtools-1.18 (although I attempted to make an environment with the specific versions even though they are out of date). Here is the error I am getting in the main command:

[E::hts_open_format] Failed to open file "/path/to/RNA_Editing/SPRINT/Output/Ctrl-03//tmp//genome_mskAG/all.bam" : No such file or directory
samtools view: failed to open "/path/to/RNA_Editing/SPRINT/Output/Ctrl-03//tmp//genome_mskAG/all.bam" for reading: No such file or directory
cp: cannot stat '/path/to/RNA_Editing/SPRINT/Output/Ctrl-03//tmp//genome_mskAG/./all.sam': No such file or directory
[E::hts_open_format] Failed to open file "/path/to/RNA_Editing/SPRINT/Output/Ctrl-03//tmp//genome_mskAG/all.bam" : No such file or directory
samtools view: failed to open "/path/to/RNA_Editing/SPRINT/Output/Ctrl-03//tmp//genome_mskAG/all.bam" for reading: No such file or directory

And here is my script:

# Find all R1 files in the fastq directory
find "$fastq_dir" -name "*_trimmed_R1.fq" | while read -r fq1; do
    # Extract sample name from R1 file without "trimmed"
    sample_name=$(basename "$fq1" | sed -E 's/_trimmed_R1.fq$//')

    # Construct R2 file path without "trimmed"
    fq2="${fastq_dir}/${sample_name}_trimmed_R2.fq"

    # Create a directory for the sample without "trimmed"
    sample_output_dir="${output_dir%/}/${sample_name}"
    mkdir -p "$sample_output_dir"

    # Print information for debugging
    echo "Sample Name: $sample_name"
    echo "Read 1: $fq1"
    echo "Read 2: $fq2"
    echo "Output Directory: $sample_output_dir"

    # Run the sprint command
    python2 "${sprint_path}/run.py" main -1 "$fq1" -2 "$fq2" -rp "${reference_dir}/ref.bed" "${reference_dir}/ref.fa" "${sample_output_dir}" "${bwa_installation}" "${samtools_installation}"

done

I don't understand there is a // in all of these paths. I even tried removing them manually in my script when I defined an output dir for each of my samples. As a result, the all.bam is not being created. I decided to see what kind of results I would get if I ran the getA2I.py since my main still finishing running with no errors other than that and created the bam files for each read. When I ran the A2I script this was the error I ran into:

IOError: [Errno 2] No such file or directory: 'path/to/RNA_Editing/SPRINT/Output/NO-01/tmp/SPRINT_identified_regular.res'

Can you please explain in detail what the inputs and outputs are for getA2I.py and how I can get around this error in the main? I am assuming they are linked because there is no .res file to be found in any of my main output folders and that seems to be what getA2I.py is taking in as an input. I also do not understand if I should literally just be passing in A_to_I_OUT or if that is a path to a directory or the name of the file I want to output to. Again, I'm just a bit confused as the manual is not very descriptive. Thanks in advance for the help.

Hi,

I used the command below :
sprint main -rp ~/my_refdata/hg19_sprint/hg19_repeat.txt -c 6 -p 12 -1 normal_11_1.fq -2 normal_11_2.fq ~/my_refdata/hg19_sprint/hg19.fa normal_11_output bwa samtools
but it takes a long time to get the results. About two days, maybe. Are there some ways to accelerate the process ?
By the way, the size of normal_11_1.fq is 23G.

Thanks.

Hi,
I have run this command assprint main -1 G1_forward_paired.fq -2 G1_reverse_paired.fq Triticum_aestivum.IWGSC.dna.toplevel.fa G1_ES bwa samtools
samtool version is 1.9 and bwa tool version 0.7.17-t1188

but I met the following errors as

[main] CMD: bwa samse -n4 Triticum_aestivum.IWGSC.dna.toplevel.fa G1_ES//tmp//genome/read2.sai G1_ES//tmp/cut_read2.fastq [main] Real time: 3829.614 sec; CPU: 3796.364 sec [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files

and then

[E::hts_open_format] Failed to open file G1_ES//tmp//genome/name_read1_sorted.bam samtools merge: fail to open "G1_ES//tmp//genome/name_read1_sorted.bam": No such file or directory [E::hts_open_format] Failed to open file G1_ES//tmp//genome/all.bam samtools view: failed to open "G1_ES//tmp//genome/all.bam" for reading: No such file or directory cp: cannot stat 'G1_ES//tmp//genome/./all.sam': No such file or directory [E::hts_open_format] Failed to open file G1_ES//tmp//genome/all.bam samtools view: failed to open "G1_ES//tmp//genome/all.bam" for reading: No such file or directory
and then

[E::hts_open_format] Failed to open file G1_ES//tmp//genome_mskAG/all.bam samtools view: failed to open "G1_ES//tmp//genome_mskAG/all.bam" for reading: No such file or directory cp: cannot stat 'G1_ES//tmp//genome_mskAG/./all.sam': No such file or directory [E::hts_open_format] Failed to open file G1_ES//tmp//genome_mskAG/all.bam samtools view: failed to open "G1_ES//tmp//genome_mskAG/all.bam" for reading: No such file or directory
and then
[E::hts_open_format] Failed to open file G1_ES//tmp//genome_mskTC/all.bam samtools view: failed to open "G1_ES//tmp//genome_mskTC/all.bam" for reading: No such file or directory cp: cannot stat 'G1_ES//tmp//genome_mskTC/./all.sam': No such file or directory [E::hts_open_format] Failed to open file G1_ES//tmp//genome_mskTC/all.bam samtools view: failed to open "G1_ES//tmp//genome_mskTC/all.bam" for reading: No such file or directory Traceback (most recent call last):

I have run A2I.py script download from github.The command is as
python A2I.py 1 ~/iQRA/sabih/G1oldversion_result/SPRINT_identified_regular.res A_to_I_OUT

I got the following error

$1: INT, 1 for strand-specific sequencing data.
$2: OUTPUT_DIR of SPRINT
$3: OUTPUT_PATH of A-to-G RESs

Traceback (most recent call last):
File "A2I.py", line 15, in
fi=open(regular)
IOError: [Errno 20] Not a directory: '/home/ngslab/iQRA/sabih/G1oldversion_result/SPRINT_identified_regular.res/SPRINT_identified_regular.res'

Hello,

I'm new to Bioinformatics, so excuse me in advance for any ambiguities I come up with. I used SPRINT to identify the RES for my RNA-seq samples and after that I used ANNOVAR to annotate the files produced by SPRINT (converted into ANNOVAR compatible format). I noticed though, that for many RES, ANNOVAR provided a different strand to the one SPRINT included in the results. My reads were pair-end. I used BWA 0.7.17 and samtools 1.2 with SPRINT. I guess aditional information is needed, so you can inform me about anything else I should provide you with, in order to solve this issue.

Thank you for your time.

Hi,

I used Sprint to identify editing sites. Same script to two samples. The IGV shows this editing site exist for both samples. But in the Sprint results, I can only find this site in the first sample, but not in the second sample. Any idea what is the problem?

Hi,
I noticed that edited reads can be extracted from "tmp/all_combined.zz". So is it possible for me to count total edited reads from all_combined.zz ? Each line in all_combined.zz file means one edited read?

Thank you.

I was successfully able to run sprint prepare but there are a lot of different output files including multiple fasta files such as .fa.mskAG.fa, .fa.mskTC.fa, .fa.trans.fa, .fa.trans.fa.mskAG.fa, and .fa.trans.fa.mskTC.fa. I understand the purpose of sprint prepare is to mask the reference genome and build a mapping index but when running sprint main are we supposed to use the same original reference fasta or use one of the reference fastas outputted from the prepare? I am confused as there is not much of an explanation as to what is going on in this step and how its output will be applied to/used in the main script. Thanks!

Hi Feng,
Thanks for developing the SPRINT.
I'm trying to find the possible RNA editing sites which may change the protein sequence with the help of SPRINT. Since I have done the RNA mapping with the STAR and gotten the sorted bam files. I use the 'sprint_from_bam.py' directly to save time.
The run process is well-going without any error information. However, the final result file contains no RNA editing information.
The command is as follows:

python /hwangxy/software/SPRINT/sprint_from_bam.py \
-rp /hwangxy/RNA_edit/data/dbrep/hg38_repeat.txt \
/RNAseq/all_bam/P001_Aligned.sortedByCoord.out.bam \
/hwangxy/reference/TCGA_GRCh38_bwa_ref/GRCh38.d1.vd1.fa \
/hwangxy/RNA_edit/result/Sprint/test_out/  \
/hwangxy/anaconda3/envs/py27/bin/samtools

The command output is like this:

And the final results files:

Other res_files in tmp directory:

The python version is 2.7.18 and samtools version is 1.2. I also can ensure that there are several RNA edit sites in my test bam file which I can see in the IGV window.

Another thing I'm not sure about is that the command was run in an HPC with 20 CPU cores and 32G Memory. But I ran several times which average time consumption is about 3.5 hours (without RNA mapping). Is this normal?

I would appreciate it if you can provide any help.
Many thanks,
Sunmile

Hi. I compared the RESs called by SPRINT and RESs from RADAR database, and find only 18% RESs are overlaped. That means many RESs called by SPRINT are not found in this database. Does this mean that the sites I found are inaccurate? Thank you.

I am trying to run SPRINT but I get errors regarding file paths

[E::hts_open_format] Failed to open file "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskTC/all.bam" : No such file or directory
samtools view: failed to open "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskTC/all.bam" for reading: No such file or directory
cp: cannot stat '/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskTC/./all.sam': No such file or directory
[E::hts_open_format] Failed to open file "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskTC/all.bam" : No such file or directory
samtools view: failed to open "/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp//genome_mskTC/all.bam" for reading: No such file or directory
Traceback (most recent call last):
  File "run.py", line 7, in <module>
  File "sprint/pipeline.py", line 42, in pipeline
  File "sprint/sprint_main.py", line 476, in main
  File "sprint/tools_sam/recover_sam.py", line 39, in recover_sam
IOError: [Errno 2] No such file or directory: '/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/sprint_output/AD1E//tmp/genome_mskAG_all.sam'
Failed to execute script run

I do not understand why it adds "/" before and after "tmp". Do you have a solution to this situation?

The command I used is:

/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/SPRINT/bin/sprint main \
-1 /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/input/SRR609422_1.fastq \
-2 /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/AD/input/SRR609422_2.fastq \
-rp /media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/SPRINT/dbrep/hg19_repeat.txt \
-c 6 \
-p 20 \
/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/hg19/hg19.fa \
AD1E \
/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/bwa-0.7.17/bwa \
/media/kokyriakidis/PRODUCTION/EDITING/SPRINT_ANALYSIS/samtools-1.13/samtools

Hi :)

I´m trying to run SPRINT via script, not from command line. The folder, I start the script in, contains sprint, bwa and samtools as subfolders. I have two questions.

1. When I´m trying to run sprint prepare and sprint main via script I get the error:
   /DIRECTION/sprint-0.1.7/sprint: Is a directory

In a previous issue, I found, that you suggested to run "chmod 777 sprint", which I ran in the sprint folder, but it didn´t resolve the problem.

Do you have an idea, what went wrong or what I could do to resolve this issue?

2. The Github page suggests, that there is "sprint_from_bam.py" in the main folder of sprint ("sprint-0.1.7"). I don´t find it in my installed folder. How could I add or execute it?

Thanks a lot in advance!

Hi, I want to get the total number of reads covering the editing site. I wonder if I counld get these from the output files. Thanks!

All sam files output by zz2sam.py ignore the sam_flag indicated in the all_combined.zz file and hard-code sam_flag 0 into the sam file. This program also outputs more reads than are present in the original all_combined.zz file. Also, many reads have an asterisk in multiple fields in the all_combined.zz file. These * containing reads contain no information about RNA-editing and yet are presumed to be RNA-edited reads based on a straight-forward reading of the SPRINT manual.

hi Jumphone,
when i run "sprint main", i met the error as below:
[huang@node6 sle2]$ mapping...
[W::sam_read1] parse error at line 1
[main_samview] truncated file.
[W::sam_read1] parse error at line 1
[main_samview] truncated file.
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
...

[W::sam_read1] parse error at line 1
[main_samview] truncated file.

and there are my script:
sprint main
-rp /home/sprint_ref/hg19_repeat.txt
-c 6 -p 2 -1 /home/sprint_ref/SRR1643011_1.fq -2 /home/sprint_ref/SRR1643011_2.fq
/home/sprint_ref/hg19.fa
/home/huang/SLE/sle2
/home/huang/analysispipeline/simulation-programs/bwa-0.6.1/bwa
/home/huang/installed/sinotools/thirdparty/samtools/samtools-1.3.1/samtools

then there is no output. I've checked the .repeat file, the .fa file, the path to bwa and samtools.
Thank you.

Hi,
I have detected the RNA editing sites by using the SPRINT tool. i have the result file in .RES format as the SPRINT generate it. i have also find the the coding gene in which these RNA editing sites are present. now i want to know about effect of these RNA editing sites on codon changes. kindly tell me how i can i find it ? i want to this type of information of my data as following

acA/acG glysine/serine
The file format is as following after finding the genes in which RNA editing sites are present.

`1A 113251747 113251748|1A 113251083 113252461 gene1 0 -

1A 113251757 113251758|1A 113251083 113252461 gene1 0 -

1A 113251774 113251775|1A 113251083 113252461 gene1 0 -

1A 113251797 113251798|1A 113251083 113252461 gene1 0 -

`

Hi,

In your paper, you have performed: "Before mapping, the first 6 bases of each read were trimmed to avoid mapping errors caused by random-hexamer primers."

Is this process included in SPRINT main?

Thanks,
Yichao

error happens with import sprint from python console

.
It should be from .tools_fq import *?

nohup sprint main -c 6 -rp Triplophysarosa.repeat.txt -1 Fish-A808-T01_good_1.fq -2 Fish-A808-T01_good_2.fq Triplophysarosa.fa Fish-A808-T01-main-rptxt /data/duanshumeng/biosoft/bwa-0.7.15/bwa /data/duanshumeng/biosoft/samtools-1.2/samtools &

This is my command.If there is no "-rp Triplophysarosa.repeat.txt " ,it worked well .However,when I add that cannot run properly.I fail to download your hg19_repeat.txt many times.

The size of my fastq files was10G+10G for pair-ended sequencing, and the function of "sprint main" with "-p 100" consuming around 12 hours to generate the result. I wonder if it was the normal time to produce the result?

I encountered a problem during SPRINT prepare stage and I failed to resolve the question.
With bwa downloaded either from your github repo or I manually downloaded, after "Building BWA index...", I consistently get the "/bin/sh: 1: pathxxx Permission denied" message in my newly installed Ubuntu 19.04.
Hope you can kindly give me some clue to fix this issue.

Hi
I have download script the zz2sam.py from this link.
[https://github.com/jumphone/SPRINT/tree/master/utilities]
I have run this command as python zz2sam.py temp/genome_all.zz.dedup
I met the following error
Traceback (most recent call last):
File "zz2sam.py", line 2, in
fi=open(sys.argv[1])
IOError: [Errno 2] No such file or directory: 'temp/genome_all.zz.dedup'
kindly suggest me how to resolve it

您好，我是一名对生物统计和生命科学比较感兴趣的信息技术从业者，目前从事信息安全和数据分析相关的领域研究，一直关注着您的项目和实验室的动态。

可是实验室的官网 http://tianlab.cn/ 以及子域从四月中旬开始就无法访问，能否留给我一个邮箱或者社交网络的id，以便联系交流？

Thx.

Hi!

Do you have a script to perform differential editing analysis (case-control samples) using the output tables of SPRINT?

Hello,
I downloaded mouse RNA-Seq data from NCBI as test data to run SPRINT. The accession code of my downloaded data is SRR1920270.
Firstly, I run SPRINT without adding repeats bed file after trim the downloaded data using Trimmomatic-0.32. There is my command below:

~/bin/SPRINT-0.1.8/bin/sprint prepare
-t ~/test/genome_file/Mus_musculus.GRCm38.96.gtf
~/test/genome_file/Mus_musculus.GRCm38.96.genome.fa
~/bin/SPRINT-0.1.8/samtools_and_bwa/bwa

~/bin/SPRINT-0.1.8/bin/sprint main -c 6 -p 10
-1 ~/test/SRR1920270-1/SRR1920270_R1.clean.fastq
-2 ~/test/SRR1920270-1/SRR1920270_R2.clean.fastq
~/test/genome_file/Mus_musculus.GRCm38.96.genome.fa
~/test/SRR1920270
~/bin/SPRINT-0.1.8/samtools_and_bwa/bwa
~/bin/SPRINT-0.1.8/samtools_and_bwa/samtools

cut -f 4 SPRINT_identified_regular.res | sort | uniq -c
53 AC
1478 AG
20 AT
33 CA
41 CG
1354 CT
1206 GA
36 GC
31 GT
21 TA
1471 TC
41 TG
1 Type

The rate of A-to-G is much less than 90% which is confict with the common conclusion in mouse. Additonally, the rates of C-to-T and G-to-A were comparable to the rate of A-to-G. I guess that perhaps SNVs were not removed in low complexity regions and simple repeats without providing repeat annotation file. And then I ran SPRINT again with repeat annotation file downloaded from UCSC. Here is my second command:

~/bin/SPRINT-0.1.8/bin/sprint main -c 6 -p 10
-rp ~/test/genome_file/mm10.repeats.bed
-1 ~/test/SRR1920270-1/SRR1920270_R1.clean.fastq
-2 ~/test/SRR1920270-1/SRR1920270_R2.clean.fastq
~/test/genome_file/Mus_musculus.GRCm38.96.genome.fa
~/test/SRR1920270
~/bin/SPRINT-0.1.8/samtools_and_bwa/bwa
~/bin/SPRINT-0.1.8/samtools_and_bwa/samtools

cut -f 4 SPRINT_identified_regular.res | sort | uniq -c
15 AC
1117 AG
25 AT
28 CA
20 CG
597 CT
546 GA
21 GC
30 GT
21 TA
1039 TC
30 TG
1 Type

The rate of A-to-G was increased but still much less than 90%. And the rates of C-to-T and G-to-A were also very high. I don't know where is the problem. Could you give me some help? Thanks!

Best regard,

I run the script below but nothing comes out, nor error message. The output folder is empty.

python ~/biosoft/SPRINT-master/sprint/sprint_prepare.py -t /path/transcript_annotation.gtf /path/reference_genome.fa ~/miniconda3/envs/rnasoft/bin/bwa;
python ~/biosoft/SPRINT-master/sprint/sprint_main -1 /path/Breast_A1_1.fq.gz -2 ./Breast_A1_2.fq.gz -p 10 /path/reference_genome.fa /path/rnaedit_output /path/bwa /path/samtools

How should I fix this? Thanks.

By using command pip install sprint I am facing error as shown below.
It is installed successfully but not working. Don't know why? working on Ubuntu 20.04 latest version.

iqra@workstation:$ pip install sprint
Collecting sprint
Downloading sprint-0.1.7.tar.gz (17 kB)
Building wheels for collected packages: sprint
Building wheel for sprint (setup.py) ... done
Created wheel for sprint: filename=sprint-0.1.7-py2.py3-none-any.whl size=32230 sha256=04993b25bed388bd35eb7f09161e112f8182f760fd4c71518b5daaaab2cdf6ff
Stored in directory: /home/iqra/.cache/pip/wheels/ee/80/71/0e23721d6b3f2383975a997f8f74c350600ce2dd6cb720b50e
Successfully built sprint
Installing collected packages: sprint
WARNING: The script sprint is installed in '/home/iqra/.local/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed sprint-0.1.7
iqra@workstation:$ sprint

Command 'sprint' not found, did you mean:

command 'qprint' from deb qprint (1.1.dfsg.2-2build1)
command 'spring' from deb ruby-spring (2.1.0-1)
command 'spring' from deb spring (104.0+dfsg-4ubuntu7)
command 'print' from deb mime-support (3.64ubuntu1)
command 'lprint' from deb lprint (1.0-1)
command 'splint' from deb splint (1:3.1.2+dfsg-1build1)

Try: sudo apt install

In your paper , there a sentence "suggesting that many one-read-count SNVs may be system errors",
So in the SPRINT output files "SPRINT_identified_all.res", which SNVs should be remove?
the SNVs with 1 supporting read, or the SNVs which AD:DP = 1:1 ?

Thank you.