Error during test data analysis

[Artem Nedoluzhko]

I have started using miARma for circular RNA ( with test data). At first, I had such a result... Can you help me?

[Thu Dec 6 09:07:04 2018] Starting a miARma analysis for circRNA [Thu Dec 6 09:07:04 2018] Checking provided parameters for: Quality,Aligner,ReadCount,DEAnalysis. [Thu Dec 6 09:07:04 2018] Checking General-output_dir parameter ... Exists! [Thu Dec 6 09:07:04 2018] The folder specified in (output_dir=Examples/basic_examples/circRNAs/results/) already exists. [Thu Dec 6 09:07:04 2018] Wait 5 seconds to overwrite the folder. Cancel otherwise: 0 [Thu Dec 6 09:07:10 2018] Continue. [Thu Dec 6 09:07:10 2018] All parameters are correct. [Thu Dec 6 09:07:10 2018] Starting Quality Analysis. [Thu Dec 6 09:07:39 2018] Quality Analysis finished. [Thu Dec 6 09:07:39 2018] No processed files are found [neither cutadapt, nor reaper nor adaptrimming folders], assuming Examples/basic_examples/circRNAs/reads/ are already processed [Thu Dec 6 09:07:39 2018] Starting a "BWA" Alignment Analysis Illegal division by zero at lib/CbBio/RNASeq/Aligner.pm line 3290, <RESULTS> line 1.

[Eduardo Andres Leon]

Dear Artem, sorry for the delay but I don't receive any notification once an issue is created. Is frustrating ..

As I see in your stat file, bwa is giving an error:

[main] CMD: bwa mem -T 19 -t 4 Genomes/Indexes/BWA/human/bwa_homo_sapiens19 Examples/basic_examples/circRNAs/reads/SRR1039517_1.fq.gz Examples/basic_examples/circRNAs/reads/SRR1039517_2.fq.gz
[main] Real time: 74.876 sec; CPU: 286.264 sec
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_flagstat_core] Truncated file? Continue anyway.

But this seem not to be important. The most strange thing is that the error you paste above is at 09:07, but bwa is aligning at 09:14 ... Are you sure that you sent me the correct log files ?

Thanks in advance

[Artem Nedoluzhko]

Thank you! I have resolved this problem yet. miARna got results. The table with information about circular RNAs quantity and file with coordinates were generated (but without mapping statistics). Please tell me, how can I use this file "circRNAs.tab" for collecting sequences of ciRNAs? Are there methods for converting it to the *.bed format?

[Eduardo Andres Leon]

Hi, In your result folder, you should have *.ciri files, which are the output of ciri. As these files includes the chromosome and the start/end coordinates, you ca use the cut command to create a bed file.

Once you have those bed files, you can use the getfasta command from bedtools to get the sequence: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html

Pleas let me know if I can close the issue.

[Artem Nedoluzhko]

Thank you! I will have some questions, but this issue should be closed