After setting up STIRRUPS and successfully rerunning the included samples, I tried running the same script over some of my own data, only to have a stream of errors flood the terminal. I was wondering if someone wouldn't mind offering me guidance on what the underlying cause could be.
I've processed several vaginal samples (V1-V2 region, aligned using SILVA reference) using Mothur's SOP, yielding a fasta file of genus-classified sequences that I'd now like to classify at species level. I thought it would be appropriate to use your reference file (vaginal_16S_V1V3_refdb1-1.fa), so the only thing I've changed in the example command is the file used in the -r option. However, I end up with the problem above, with the output looking like this:
Parsing USEARCH output...
Use of uninitialized value $read_id in string ne at stirrups_pipeline_1.0.pl line 230, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 323, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 324, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 325, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 326, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 327, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 328, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 329, <FH> line 1.
Use of uninitialized value $prev_id in string ne at stirrups_pipeline_1.0.pl line 230, <FH> line 2.
Use of uninitialized value $read_id in string ne at stirrups_pipeline_1.0.pl line 230, <FH> line 2.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 2.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 2.
Use of uninitialized value $prev_id in string ne at stirrups_pipeline_1.0.pl line 230, <FH> line 3.
Use of uninitialized value $read_id in string ne at stirrups_pipeline_1.0.pl line 230, <FH> line 3.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 3.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 3.
...
Use of uninitialized value $prev_id in concatenation (.) or string at stirrups_pipeline_1.0.pl line 277, <FH> line 918512.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 918512.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 918512.
OUTPUT Assignment File = stability.trim.contigs.good.unique.good.filter.unique.precluster.pick_assignment_97.txt
Unfortunately I'm at a loss for how to go about solving this issue, since Google has failed me. If someone could kindly point me in the right direction or has a working solution, I'd greatly appreciate your feedback.
Best,
Michael Frisch
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After setting up STIRRUPS and successfully rerunning the included samples,
I tried running the same script over some of my own data, only to have a
stream of errors flood the terminal. I was wondering if someone wouldn't
mind offering me guidance on what the underlying cause could be.
I've processed several vaginal samples (V1-V2 region, aligned using SILVA
reference) using Mothur's SOP, yielding a fasta file of genus-classified
sequences that I'd now like to classify at species level. I thought it
would be appropriate to use your reference file
(vaginal_16S_V1V3_refdb1-1.fa), so the only thing I've changed in the
example command is the file used in the -r option. However, I end up with
the problem above, with the output looking like this:
Parsing USEARCH output...
Use of uninitialized value $read_id in string ne at
stirrups_pipeline_1.0.pl line 230, <FH> line 1.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 322, <FH> line 1.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 323, <FH> line 1.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 324, <FH> line 1.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 325, <FH> line 1.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 326, <FH> line 1.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 327, <FH> line 1.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 328, <FH> line 1.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 329, <FH> line 1.
Use of uninitialized value $prev_id in string ne at
stirrups_pipeline_1.0.pl line 230, <FH> line 2.
Use of uninitialized value $read_id in string ne at
stirrups_pipeline_1.0.pl line 230, <FH> line 2.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 322, <FH> line 2.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 322, <FH> line 2.
Use of uninitialized value $prev_id in string ne at
stirrups_pipeline_1.0.pl line 230, <FH> line 3.
Use of uninitialized value $read_id in string ne at
stirrups_pipeline_1.0.pl line 230, <FH> line 3.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 322, <FH> line 3.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 322, <FH> line 3.
...
Use of uninitialized value $prev_id in concatenation (.) or string at
stirrups_pipeline_1.0.pl line 277, <FH> line 918512.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 322, <FH> line 918512.
Use of uninitialized value $read_id in hash element at
stirrups_pipeline_1.0.pl line 322, <FH> line 918512.
OUTPUT Assignment File =
stability.trim.contigs.good.unique.good.filter.unique.precluster.pick_assignment_97.txt
Unfortunately I'm at a loss for how to go about solving this issue, since
Google has failed me. If someone could kindly point me in the right
direction or has a working solution, I'd greatly appreciate your feedback.
Hi there Fettweis Lab,
After setting up STIRRUPS and successfully rerunning the included samples, I tried running the same script over some of my own data, only to have a stream of errors flood the terminal. I was wondering if someone wouldn't mind offering me guidance on what the underlying cause could be.
I've processed several vaginal samples (V1-V2 region, aligned using SILVA reference) using Mothur's SOP, yielding a fasta file of genus-classified sequences that I'd now like to classify at species level. I thought it would be appropriate to use your reference file (vaginal_16S_V1V3_refdb1-1.fa), so the only thing I've changed in the example command is the file used in the -r option. However, I end up with the problem above, with the output looking like this:
Parsing USEARCH output...
Use of uninitialized value $read_id in string ne at stirrups_pipeline_1.0.pl line 230, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 323, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 324, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 325, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 326, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 327, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 328, <FH> line 1.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 329, <FH> line 1.
Use of uninitialized value $prev_id in string ne at stirrups_pipeline_1.0.pl line 230, <FH> line 2.
Use of uninitialized value $read_id in string ne at stirrups_pipeline_1.0.pl line 230, <FH> line 2.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 2.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 2.
Use of uninitialized value $prev_id in string ne at stirrups_pipeline_1.0.pl line 230, <FH> line 3.
Use of uninitialized value $read_id in string ne at stirrups_pipeline_1.0.pl line 230, <FH> line 3.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 3.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 3.
...
Use of uninitialized value $prev_id in concatenation (.) or string at stirrups_pipeline_1.0.pl line 277, <FH> line 918512.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 918512.
Use of uninitialized value $read_id in hash element at stirrups_pipeline_1.0.pl line 322, <FH> line 918512.
OUTPUT Assignment File = stability.trim.contigs.good.unique.good.filter.unique.precluster.pick_assignment_97.txt
Unfortunately I'm at a loss for how to go about solving this issue, since Google has failed me. If someone could kindly point me in the right direction or has a working solution, I'd greatly appreciate your feedback.
Best,
Michael Frisch
Hi Michael,
Is it possible for you to share your fasta file ? Also, can you please
check the version of usearch you are using ?
Thanks,
Nihar
On Tue, Dec 1, 2015 at 4:03 PM, Michael Frisch mfrisch3@users.sf.net
wrote:
Hi Nihar,
I can share a sample of it, see attached. I'm running usearch v5.2.32.
Best,
Michael Frisch
Hi Michael,
Thanks for sharing the file and information regarding the version. I will
run your file with our local installation and let you know the results.
Thanks,
Nihar
On Wed, Dec 2, 2015 at 10:30 AM, Michael Frisch mfrisch3@users.sf.net
wrote: