Error when execute archer tool inside galaxy

Question: Error when execute archer tool inside galaxy

4.5 years ago by

GPS • 20

India

GPS • 20 wrote:

Hello everyone

I am trying to integrate and execute the archer analysis pipeline tool into galaxy project for that I write the XML file and execute the archer but galaxy will show error please any one tell me solution on this error.

<?xml version="1.0"?>
<tool id="archerTool" name="archer">
<description>for each sequence in a file</description>
<command> /home/archer_1.0.0/archer/archer.pl -config $file_data</command>
<inputs>
<param name="file_data" type="data" format="dat" />
</inputs>
<outputs>
<data format="dat" name="out_file1" />
</outputs>
<help>
</help>
</tool>

Error display by galaxy:

[M::main_mem] read 2 sequences (300 bp) from /home/archer_1.0.0pre/bwa_enz/tests//test2.fastq...
[main] Version: 0.7.5a-r418, modified to simplify gene fusion detection by Enzymatics
[main] CMD: bwa_enz mem -Q 0 -m -D /home/archer_1.0.0pre/bwa_enz/tests/ /home/archer_1.0.0pre/chromFa/hg19.fa /home/archer_1.0.0pre/bwa_enz/tests//test2.fastq
[main] Real time: 972.034 sec; CPU: 7.668 sec
Traceback (most recent call last):
  File "/home/plus91/archer_1.0.0pre/archer/get_median_quality.py", line 32, in <module>
    for read in reader:
  File "/usr/local/lib/python2.7/dist-packages/HTSeq/__init__.py", line 407, in __iter__
    raise ValueError( "Primary and secondary ID line in FASTQ"
ValueError: Primary and secondary ID line in FASTQdisagree.
Error: The requested bed file (/home/plus91/archer_1.0.0pre/bwa_enz/tests//test2.dedup.points.bed) could not be opened. Exiting!
BgzfStream ERROR: read block failed - invalid block header
BamHeader ERROR: could not read magic number
BamReader ERROR: Could not load header data for /dev/stdin
BgzfStream ERROR: read block failed - invalid block header
BamHeader ERROR: could not read magic number
BamReader ERROR: Could not load header data for /dev/stdin
Segmentation fault (core dumped)
Illegal division by zero at /home/archer_1.0.0pre/archer/counts_2.pl line 130.
cat: /home/archer_1.0.0pre/bwa_enz/tests//test2.counts.dat: No such file or directory
cat: /home/archer_1.0.0pre/bwa_enz/tests//test2.counts.machine.dat: No such file or directory
rm: cannot remove `/home/archer_1.0.0pre/bwa_enz/tests//test2.counts.dat': No such file or directory
rm: cannot remove `/home/archer_1.0.0pre/bwa_enz/tests//test2.counts.machine.dat': No such file or directory

Thank You

GPS

tool bwa galaxy samtools • 1.9k views

ADD COMMENT • link •

modified 4.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.5 years ago by GPS • 20

Hi GPS,

please make sure you are able to run this tool on command line and you know what it does. It seems it stores some data in a tests folder or something like that. At least the files test2.counts.* could not be found, so it is not a Galaxy problem.

Cheers,

Bjoern

ADD REPLY • link written 4.5 years ago by Bjoern Gruening ♦ 5.1k

4.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Are you working with the user that reported this problem today, a bit earlier than you? bwa_enz not found in archer analysis pipeline
If so, then these two posts should probably be merged.

Advice and links are in the reply to that thread. Running the tool successfully on the command-line is the first step. It is not clear from these errors if that has been successful with these same inputs or not. The successive errors are likely derivatives of earlier execution errors. If the errors are with this specialized version of BWA, the documentation for the tool has instructions for troubleshooting (online).

Best, Jen, Galaxy team

ADD COMMENT • link written 4.5 years ago by Jennifer Hillman Jackson ♦ 25k

Hello Jennifer,

Thank you for your reply i solve the bwa_enz not found in archer analysis pipeline error but now i have some error has been occur

so please tell me how i solve that error.

[M::main_mem] read 2 sequences (300 bp) from /home/plus91/archer_1.0.0pre/bwa_enz/tests//test2.fastq...

[main] Version: 0.7.5a-r418, modified to simplify gene fusion detection by Enzymatics
[main] CMD: bwa_enz mem -Q 0 -m -D /home/archer_1.0.0pre/bwa_enz/tests/ /home/archer_1.0.0pre/chromFa/hg19.fa 
/home/archer_1.0.0pre/bwa_enz/tests//test2.fastq
[main] Real time: 918.478 sec; CPU: 7.660 sec
Traceback (most recent call last):
  File "/home/archer_1.0.0pre/archer/get_median_quality.py", line 32, in <module>
    for read in reader:
  File "/usr/local/lib/python2.7/dist-packages/HTSeq/__init__.py", line 407, in __iter__
    raise ValueError( "Primary and secondary ID line in FASTQ"
ValueError: Primary and secondary ID line in FASTQdisagree.
Error: The requested bed file (/home/archer_1.0.0pre/bwa_enz/tests//test2.dedup.points.bed) could not be opened. Exiting!
BgzfStream ERROR: read block failed - invalid block header
BamHeader ERROR: could not read magic number
BamReader ERROR: Could not load header data for /dev/stdin
BgzfStream ERROR: read block failed - invalid block header
BamHeader ERROR: could not read magic number
BamReader ERROR: Could not load header data for /dev/stdin
Segmentation fault (core dumped)
Illegal division by zero at /home/archer_1.0.0pre/archer/counts_2.pl line 130.
cat: /home/archer_1.0.0pre/bwa_enz/tests//test2.counts.dat: No such file or directory
cat: /home/archer_1.0.0pre/bwa_enz/tests//test2.counts.machine.dat: No such file or directory
rm: cannot remove `/home/archer_1.0.0pre/bwa_enz/tests//test2.counts.dat': No such file or directory
rm: cannot remove `/home/archer_1.0.0pre/bwa_enz/tests//test2.counts.machine.dat': No such file or directory

Thank You

GPS

ADD REPLY • link written 4.5 years ago by GPS • 20

Hello GPS,

It is still not clear if the two questions for this tool are related. Would you be able to help us out to know? It is easier to troubleshoot in a single thread.

In the other thread, advice was given to double check the paths to the inputs and to also to specifically check the command-line (both to see if it ran independently and to check for path errors) in the first reply. Then later replies to this thread and the other have also asked the same. It is not clear if this has been done. Would you be able to help us with this, so that we can know how to help you?

Just from looking here - it may be that an extra trailing "/" slash in the command-line is causing a path problem - this is most likely where the double "//" is coming from and why your files are not found. But please help us by consolidating the questions and working through the troubleshooting in a logical order, letting who is helping you know how prior advice worked: executables in place, can execute command-line, duplicate that execution the wrapper.

We want to help you and hopefully following this method will be successful, Best, Jen, Galaxy team

ADD REPLY • link written 4.5 years ago by Jennifer Hillman Jackson ♦ 25k

Hello Jennifer

Thank you for the reply .

I download the archer tool then try to integrate that tool into galaxy before integration archer tool in galaxy I executing that tool on the command line and i got this error on command line as I post earlier .

and I also try by removing extra "/" slash but still i get the same error please tell me the solution on this.

[M::main_mem] read 2 sequences (300 bp) from /home/archer_1.0.0pre/bwa_enz/tests//test2.fastq...
[main] Version: 0.7.5a-r418, modified to simplify gene fusion detection by Enzymatics
[main] CMD: bwa_enz mem -Q 0 -m -D /home/archer_1.0.0pre/bwa_enz/tests/ /home/archer_1.0.0pre/chromFa/hg19.fa 
/home/archer_1.0.0pre/bwa_enz/tests//test2.fastq
[main] Real time: 972.034 sec; CPU: 7.668 sec
Traceback (most recent call last):
  File "/home/archer_1.0.0pre/archer/get_median_quality.py", line 32, in <module>
    for read in reader:
  File "/usr/local/lib/python2.7/dist-packages/HTSeq/__init__.py", line 407, in __iter__
    raise ValueError( "Primary and secondary ID line in FASTQ"
ValueError: Primary and secondary ID line in FASTQdisagree.
Error: The requested bed file (/home/archer_1.0.0pre/bwa_enz/tests//test2.dedup.points.bed) could not be opened. Exiting!
BgzfStream ERROR: read block failed - invalid block header
BamHeader ERROR: could not read magic number
BamReader ERROR: Could not load header data for /dev/stdin
BgzfStream ERROR: read block failed - invalid block header
BamHeader ERROR: could not read magic number
BamReader ERROR: Could not load header data for /dev/stdin
Segmentation fault (core dumped)
Illegal division by zero at /home/plus91/archer_1.0.0pre/archer/counts_2.pl line 130.
cat: /home/archer_1.0.0pre/bwa_enz/tests//test2.counts.dat: No such file or directory
cat: /home/archer_1.0.0pre/bwa_enz/tests//test2.counts.machine.dat: No such file or directory
rm: cannot remove `/home/archer_1.0.0pre/bwa_enz/tests//test2.counts.dat': No such file or directory
rm: cannot remove `/home/archer_1.0.0pre/bwa_enz/tests//test2.counts.machine.dat': No such file or directory

Thank You

GPS

ADD REPLY • link written 4.5 years ago by GPS • 20

Can you verify the file exists that's being referred to in the error message you're pasting?

It does look like you're still having extra slashes appear all over. Please do recheck your path writing within the tool.

ADD REPLY • link written 4.5 years ago by Dannon Baker ♦ 3.7k

I know nothing about the particular package, but it seems to be calling your local python's HTSeq code and throwing:

ValueError: Primary and secondary ID line in FASTQdisagree.

That seems to imply a broken fastq file which seems odd if it's the test file.

Does this work correctly on your system from the command line? In my experience, before you start wrapping a new Galaxy tool, it's best to get it working correctly without the extra complications that Galaxy adds?

ADD REPLY • link written 4.5 years ago by fubar ♦ 1.1k

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