Scripts and Files used:

• renameBams.sh
• sbatch-doIt.sh
• S_lycopersicum_Jun_2022.2bit
• S_lycopersicum_Sep_2019.2bit
• find_junctions.sh
• find-junctions-1.0.0-jar-with-dependencies.jar
• bamCoverage.sh

Launch renameBams.sh script:

./renameBams.sh

Launch Scaled Coverage graphs script:

./sbatch-doIt.sh .bam bamCoverage.sh >jobs.out 2>jobs.err

Launch Junction files script:

./sbatch-doIt.sh .bam find_junctions.sh >jobs.out 2>jobs.err

SL5 Directory: /nobackup/tomato_genome/Ravi_2022/Ravi_2022_SL5/results/star_salmon
SL4 Directory: /nobackup/tomato_genome/Ravi_2022/Ravi_2022_SL4/results/star_salmon

Reviewer:
Check that files have reasonable sizes (no "zero" size files, for example)
Check that every "FJ.bed.gz" file has a corresponding "FJ.bed.gz.tbi" index file
Check that every bam file has a corresponding "FJ.bed.gz" file
Check that every bam file has a corresponding "scaled.bedgraph.gz" file
Check that every "scaled.bedgraph.gz" has a corresponding "scaled.bedgraph.gz.tbi"
If all files are normal please move ticket to done

*For /nobackup/tomato_genome/Ravi_2022/Ravi_2022_SL5/results/star_salmon
*
There are 1347 total files.
ll*bed.gz produces 55 gzipped bed files.
Most of these files are 5-8MB in size.

But with 2 exceptions:
rw-rr- 1 mdavi258 tomato_genome 28 Jul 25 14:44 Nagcarlang-R1-3hr-25C.FJ.bed.gz
rw-rr- 1 mdavi258 tomato_genome 699K Jul 25 14:44 Malintka-R3-8hr-37C.FJ.bed.gz

These 2 are MUCH smaller than the rest.
There are 55 .tbi files.

There are 56 .out files (1 extra for jobs.out so that makes sense).
All are similar size except for Malintka-R3-8hr-37C.out, which is only 1.9M. Not surprising given that the corresponding bed file is small / truncated. However the tiny Nag file appers to have a normal sized out file! A mystery side quest to pursue!

*ll *err CHECKING THE ERR files *
There are 56 err files as expected.
All are empty except for:
rw-rr- 1 mdavi258 tomato_genome 234 Jul 25 13:56 Tamaulipas-R1-3hr-37C.err
rw-rr- 1 mdavi258 tomato_genome 696 Jul 25 14:44 Nagcarlang-R1-3hr-25C.err
rw-rr- 1 mdavi258 tomato_genome 655 Jul 25 14:44 Malintka-R3-8hr-37C.err
rw-rr- 1 mdavi258 tomato_genome 655 Jul 25 14:44 Heinz-R3-8hr-25C.err

(our 2 previous devious samples and now 2 more!!!)

The error within:
Exception in thread "main" java.io.IOException: Cannot send after transport endpoint shutdown
at java.io.RandomAccessFile.readBytes(Native Method)
at java.io.RandomAccessFile.read(RandomAccessFile.java:400)
at org.biojava.nbio.genome.parsers.twobit.TwoBitParser.loadBits(TwoBitParser.java:205)
at org.biojava.nbio.genome.parsers.twobit.TwoBitParser.skip(TwoBitParser.java:281)
at org.biojava.nbio.genome.parsers.twobit.TwoBitParser.setCurrentSequencePosition(TwoBitParser.java:196)
at org.biojava.nbio.genome.parsers.twobit.TwoBitParser.loadFragment(TwoBitParser.java:332)
at org.lorainelab.findjunctions.FindJunctions.main(FindJunctions.java:248)
Heinz-R3-8hr-25C.err lines 1-8/8 (END)

SL4 Check
/nobackup/tomato_genome/Ravi_2022/Ravi_2022_SL4/results/star_salmon

This time starting with err files:
Found the expected 56 files. (55 + 1 jobs.err file)
Only 2 files have issues.
rw-rr- 1 mdavi258 tomato_genome 370 Jul 25 16:09 Malintka-R2-8hr-37C.err
rw-rr- 1 mdavi258 tomato_genome 370 Jul 25 16:09 Nagcarlang-R2-8hr-37C.err

No overlap from the SL5 run it seems.
But potential issues with these 2.

I find 55 bed.gz files and 55 tbi files.
All bed and tbi files are of similar size.

The err files:

Exception in thread "main" java.lang.RuntimeException: Postion is too high (more than 64792705)
at org.biojava.nbio.genome.parsers.twobit.TwoBitParser.setCurrentSequencePosition(TwoBitParser.java:191)
at org.biojava.nbio.genome.parsers.twobit.TwoBitParser.loadFragment(TwoBitParser.java:332)
at org.lorainelab.findjunctions.FindJunctions.main(FindJunctions.java:249)
Malintka-R2-8hr-37C.err lines 1-4/4 (END)

Exception in thread "main" java.lang.RuntimeException: Postion is too high (more than 64792705)
at org.biojava.nbio.genome.parsers.twobit.TwoBitParser.setCurrentSequencePosition(TwoBitParser.java:191)
at org.biojava.nbio.genome.parsers.twobit.TwoBitParser.loadFragment(TwoBitParser.java:332)
at org.lorainelab.findjunctions.FindJunctions.main(FindJunctions.java:249)
Nagcarlang-R2-8hr-37C.err lines 1-4/4 (END)

Same error for both.

Let the Scooby mystery begin!

Thank you for catching the errors Dr. Reid!

Next step: Remove the 2bit files and copy them again into the directory and rerun the junction script for SL4 & SL5. Also need to rerun scaled coverage script due to files missing.

Fixed 2bit errors:
SL5 Directory: /nobackup/tomato_genome/Ravi_2022/Ravi_2022_SL5/results/star_salmon
SL4 Directory: /nobackup/tomato_genome/Ravi_2022/Ravi_2022_SL4/results/star_salmon

Note: There is an exception/error for two files in SL4 due to positioning (Exception in thread "main" java.lang.RuntimeException: Postion is too high (more than 64792705)). Due to this being an exception I believe we can move forward with the files. Then there is also one error file in SL5 "Tamaulipas-R1-3hr-37C.err" but this is also a warning and seems to not affect the final results.

Reviewer:
Check that files have reasonable sizes (no "zero" size files, for example)
Check that every "FJ.bed.gz" file has a corresponding "FJ.bed.gz.tbi" index file
Check that every bam file has a corresponding "FJ.bed.gz" file
Check that every bam file has a corresponding "scaled.bedgraph.gz" file
Check that every "scaled.bedgraph.gz" has a corresponding "scaled.bedgraph.gz.tbi"
If all files are normal please move ticket to done

The 2 new locations for the data is NOW:

/projects/tomato_genome/fnb/Ravi_2022/Ravi_2022_SL5/results/star_salmon
/projects/tomato_genome/fnb/Ravi_2022/Ravi_2022_SL4/results/star_salmon

Our
/nobackup
is no more.

SL5:
I see 55 bedgraph and 55 bed files. All zipped and all similar size. (e.g., the bed files 6-8MB and bedgraphs bigger)

The .tbi files follow the same pattern.

All BAM files are over 1GB in size.
55 bam files. 55 bai files

SL4:
I see:
55 .tbi files for bed.gz
55 .tbi files for bedgraph.gz

All BAM files are over 1GB in size.
55 bam files. 55 bai files

All looks great!!!!!