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Install not quite correct about tabsat HOT 21 CLOSED

jamlover avatar jamlover commented on August 18, 2024
Install not quite correct

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Comments (21)

jamlover avatar jamlover commented on August 18, 2024

9-28_miseq.test.txt
Hi. I've continued to play around without success. This is what the miseq test run output looks like as of today. I think it may be slightly different than the one from the other day so I thought I'd attach it. The bottom line is still no success though.

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tadKeys avatar tadKeys commented on August 18, 2024

Dear John,

thanks for your feedback on TABSAT. I took a look at your output files and it seems to be an issue with the mapping.

Could you please send me the output of:

/media/MyBook/progs/tabsat-master/tools/samtools/samtools-1.4/samtools view /media/MyBook/progs/tabsat-master/tabsat_test_output_miseq/SRR3296596_1_NONDIR_bowtie2/SRR3296596_trimmed_1.fastq_bismark_bt2_pe.sam_removed_cov_one_sorted.bam | head

Furthermore, could you send me the output of this command as well:

head /media/MyBook/progs/tabsat-master/tabsat_test_output_miseq/SRR3296596_1_NONDIR_bowtie2/SRR3296596_trimmed_1.fastq

Thanks,
Stephan

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jamlover avatar jamlover commented on August 18, 2024

Stephan,

Here you go.

jmartins@d2626ujmartins3 zz_test]$ media/MyBook/progs/tabsat-master/tools/samtools/samtools-1.4/samtools view /media/MyBook/progs/tabsat-master/tabsat_test_output_miseq/SRR3296596_1_NONDIR_bowtie2/SRR3296596_trimmed_1.fastq_bismark_bt2_pe.sam_removed_cov_one_sorted.bam | head
bash: media/MyBook/progs/tabsat-master/tools/samtools/samtools-1.4/samtools: No such file or directory
[jmartins@d2626ujmartins3 zz_test]$ head /media/MyBook/progs/tabsat-master/tabsat_test_output_miseq/SRR3296596_1_NONDIR_bowtie2/SRR3296596_trimmed_1.fastq
@SRR3296596.1 1 length=150
GTGTGTTTTTTGTGGTTAGGTTGTATTTGTTGTTGGTGTTGATGTTATTGTTTTCGCGTTGTTAGCGTATTTTCATTTTTGTTTGTTTTGTTTTGGTTTTGAATATGGTAGGGTTGTTTGTGGTTATTTTTATTGATCGTGGTTTTTTGT
+SRR3296596.1 1 length=150

AAAACFFFBBBFGGFEFGFFGHGGHHHHGHHHHHHEFFEHFHHHHGHHHHHHHHGGGGGGGHGHHGBEGHHHHGHHHHHGGHHHFHHHHHHHHHGGHHGHGHHHHHHHHHGGFHGGHHHGHGGGGHHHHHHHHHFGHGHHGGFHGGGGH
@SRR3296596.2 2 length=150
AGGTTTTGTTTTTGGGTAAGTTATAGTTAAATGATATGTTGGTGAATGTAATCGGATGATTTTTCGGGTATTGATAAGATTTTTAAGTGTGTGTTTGGTTTCGTAGAGTTAATGGAGAGTAGGTATTTAGTCGTTTGCGGAGTAGAGTTT
+SRR3296596.2 2 length=150
AAAAAB?FBF1CFEAE1BFGAB3A3FHFH3AFFFG2EGHFFH0BFFDHGADDGFG?GGBBGHBH0F?EBA1GFD2BFBB2GGHHE@G2DGG>BFGFEFEGHHECHGGGGDFFHHFEGEEHFGH1GGHFHH1>EFEFF1EGBCCFGHH@GF
@SRR3296596.3 3 length=150
AGGTTTTGTTTTTGGGTAAGTTATAGTTAAATGATATGTTGGTGAATGTAATCGGATGATTTTTCGGGTATTGATAAGATTTTTAAGTGTGTGTTTGGTTTCGTAGAGTTAATGGAGAGTAGGTATTTAGTCGTTTGCGGAGTAGAGTTT

I also attached the output stream from my latest miseq test today. It appears to be the same as previous runs I think but just want to make sure you have
10-1-18.miseq.test.txt
the latest.

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tadKeys avatar tadKeys commented on August 18, 2024

Hi,

thanks for the answer. Could you please rerun this command, it seems you missed the first "/":

/media/MyBook/progs/tabsat-master/tools/samtools/samtools-1.4/samtools view -h /media/MyBook/progs/tabsat-master/tabsat_test_output_miseq/SRR3296596_1_NONDIR_bowtie2/SRR3296596_trimmed_1.fastq_bismark_bt2_pe.sam_removed_cov_one_sorted.bam | head

Thanks,
Stephan

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jamlover avatar jamlover commented on August 18, 2024

Oops. Sorry about that. Here is the correct command and output.

/media/MyBook/progs/tabsat-master/tools/samtools/samtools-1.4/samtools view -h /media/MyBook/progs/tabsat-master/tabsat_test_output_miseq/SRR3296596_1_NONDIR_bowtie2/SRR3296596_trimmed_1.fastq_bismark_bt2_pe.sam_removed_cov_one_sorted.bam | head
@hd VN:1.0 SO:coordinate
@sq SN:1 LN:249250621
@sq SN:10 LN:135534747
@sq SN:11 LN:135006516
@sq SN:12 LN:133851895
@sq SN:13 LN:115169878
@sq SN:14 LN:107349540
@sq SN:15 LN:102531392
@sq SN:16 LN:90354753
@sq SN:17 LN:81195210

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tadKeys avatar tadKeys commented on August 18, 2024

Hi,

could you please run this command (head with more output lines):

/media/MyBook/progs/tabsat-master/tools/samtools/samtools-1.4/samtools view -h /media/MyBook/progs/tabsat-master/tabsat_test_output_miseq/SRR3296596_1_NONDIR_bowtie2/SRR3296596_trimmed_1.fastq_bismark_bt2_pe.sam_removed_cov_one_sorted.bam | head -n 250

Thanks,
Stephan

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jamlover avatar jamlover commented on August 18, 2024

Stephan,

As requested: Output of samtools command (attached as .txt file).
samtools.view-h.command.250.lines.txt

Thanks,

John

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tadKeys avatar tadKeys commented on August 18, 2024

Hi John,

sofar I don't know exactly what's going wrong - could you please send me the output of

ls -lR /media/MyBook/progs/tabsat-master/tabsat_test_output_miseq/

Thanks and best wishes,
Stephan

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jamlover avatar jamlover commented on August 18, 2024

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tadKeys avatar tadKeys commented on August 18, 2024

Hi John,

unfortunately I don't know whats going wrong. Would it be possible for you to zip the "/media/MyBook/progs/tabsat-master/tabsat_test_output_miseq/" folder and send it to me?

Thanks,
Stephan

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jamlover avatar jamlover commented on August 18, 2024

Stephan,

Hmmm. It's about 430 MB, so I don't know exactly how I can get that to you. Actually, now that I think about it, if you have a Microsoft account I can probably share it via OneDrive. I will need an email address associated with your Microsoft account in order to do that. If you don't already have a Microsoft account, I believe it's very easy to establish one. Please advise.

Thanks,

John

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tadKeys avatar tadKeys commented on August 18, 2024

Hi John,

yes, I do have a microsoft account - please use this email address:
[email protected]

Thanks,
Stephan

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jamlover avatar jamlover commented on August 18, 2024

Stephan,

I sent the OneDrive link. Hopefully it works. The md5 for the file is 37245f8f2e32124c3b2bbd85263554cb.

Thanks,

John

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tadKeys avatar tadKeys commented on August 18, 2024

Hi John,

thanks for sending the file - I think I know now what's going wrong. As far as I can tell it's the used reference. TABSAT was developed and tested with a reference where the names of the chromosomes start with a "chr" prefix. It seems that your reference does not use one. Could you please try and change the TABSAT setup to a reference that uses a "chr" prefix?

In the meantime, we will work on TABSAT to accept both versions.

Thanks and best wishes,
Stephan

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tadKeys avatar tadKeys commented on August 18, 2024

Hi John,

I just pushed a new update with a fix. Please let me know if it works.

Best wishes,
Stephan

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jamlover avatar jamlover commented on August 18, 2024

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jamlover avatar jamlover commented on August 18, 2024

I'm not so sure about my duplicated field name idea anymore, so I thought I'd share the output generated at the lollipop stage. Please let me know if you have any ideas about this one. Thanks again.

-- Create lollipop plots for every target
Rscript --vanilla /media/MyBook/progs/tabsat-master/tools/ait/lollipop.R /media/MyBook/progs/tabsat-master/tabsat_test_output_miseq/COVERAGE_NONDIR_bowtie2 NONDIR bowtie2
$pos1
NULL

$pos2
NULL

$pos3
NULL

$pos4
NULL

$pos5
NULL

$pos6
NULL

[1] "Plotting adapted"
Error in levels<-(*tmp*, value = as.character(levels)) :
factor level [2] is duplicated
Calls: plotting -> factor
Execution halted
-- .. done with plotting.

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tadKeys avatar tadKeys commented on August 18, 2024

Hi,

do you have any update on the issue? In the meantime I tested it on my server and it's giving me a slightly different output

-- Create lollipop plots for every target
Rscript --vanilla /home/app/my_version/tabsat/tools/ait/lollipop.R /home/app/my_version/tabsat/tabsat_test_output_miseq/COVERAGE_NONDIR_bowtie2 NONDIR bowtie2 
Loading required package: methods
NULL
$pos1
NULL

$pos2
NULL

$pos3
NULL

$pos4
NULL

$pos5
NULL

$pos6
NULL

[1] "Plotting adapted"
[1] "Done with printing"

"Loading required package: methods"

Could you please send me these files from the "COVERAGE_NONDIR_bowtie2" folder

  • ResultMethylList.csv
  • MethylList.csv

Thanks and best wishes,
Stephan

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jamlover avatar jamlover commented on August 18, 2024

Stephan,

I haven't had much time to work on this the last week, so I have no updates. I'm definitely still hoping to get it working fully though. I've attached the requested files.

Thanks,
John
MethylList.csv.txt
ResultMethylList.csv.txt

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tadKeys avatar tadKeys commented on August 18, 2024

Dear John,

I pushed a new version of TABSAT that includes a fix for the lollipop issue.
Please let me know if this works for you.

Best wishes,
Stephan

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jamlover avatar jamlover commented on August 18, 2024

Stephan,

It worked! So we can close this issue.

I will mention now that my hope/plan is to import a draft genome (produced by our group) of another organism into tabsat and see if I can get it to also function error-free. Well, actually, I've already pretty much done the importing and have most of the functions working with a few errors cropping up. I'm thinking I will try debugging those on my own since I know the pipeline is working correctly on the test data. I will let you know if I end up having success in my efforts in the end.

Thanks again for your help,
John

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