search

fanagislab / EndHiC

EndHic is a fast and easy-to-use Hi-C scaffolding tool, using the Hi-C links from contig end regions instead of whole contig regions to assemble large contigs into chromosomal-level scaffolds.
19 stars 3 forks source link

Error Moving Summary Files and Reporting Total Cluster Number #10

Closed kbarslan closed 9 months ago

kbarslan commented 9 months ago

Thanks for this amazing tool!

I'm facing a problem while running; it reads the ICED matrix file. Creates and places a summary for all contig end iterations in the respective folders. In the script, it tries to move these files to another directory, but it cannot locate the file (e.g., mv: cannot stat 'X.hicpro.ICE.100000.10.results.summary': No such file or directory). Even though the files are in the Round_A.04.summary_and_merging_results directory. I think that's why it cannot report the total cluster number for the ICED matrix, as shown below.

Contig end size: 100000 x 5 Times: 1.5 2.0 2.5 3.0 3.5 4.0 4.5 Raw: 504 505 505 507 509 509 513 Iced:

Contig end size: 100000 x 10 Times: 1.5 2.0 2.5 3.0 3.5 4.0 4.5 Raw: 411 411 412 414 418 426 434 Iced:

I would appreciate any insights into why it is failing to locate and move the summary files correctly. Additionally, suggestions for troubleshooting would be very helpful.

fanagislab commented 9 months ago

Please try the testing data first. And make sure your data format and directory structure is same with the testing data.

@.***

From: kbarslan Date: 2024-02-06 21:43 To: fanagislab/EndHiC CC: Subscribed Subject: [fanagislab/EndHiC] Error Moving Summary Files and Reporting Total Cluster Number (Issue #10) Thanks for this amazing tool! I'm facing a problem while running; it reads the ICED matrix file. Creates and places a summary for all contig end iterations in the respective folders. In the script, it tries to move these files to another directory, but it cannot locate the file (e.g., mv: cannot stat 'X.hicpro.ICE.100000.10.results.summary': No such file or directory). I think that's why it cannot report the total cluster number for the ICED matrix, as shown below. Contig end size: 100000 x 5 Times: 1.5 2.0 2.5 3.0 3.5 4.0 4.5 Raw: 504 505 505 507 509 509 513 Iced: Contig end size: 100000 x 10 Times: 1.5 2.0 2.5 3.0 3.5 4.0 4.5 Raw: 411 411 412 414 418 426 434 Iced: I would appreciate any insights into why it is failing to locate and move the summary files correctly. Additionally, suggestions for troubleshooting would be very helpful. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>

kbarslan commented 9 months ago

Thank you for the answer!

The test data is working but I think my issue was my file names.

Old names; L1.mapped.pairs.100000.hicpro L1.mapped.pairs.100000.hicpro.ICE L1.mapped.pairs.100000.hicpro.bed ref.genome

Then I tried naming my files as test data file names.

New names; Fba.contigs.fa FbaHiC_100000.matrix FbaHiC_100000_abs.bed FbaHiC_100000_iced.matrix

After that, the analysis ran without any problems.