stuck on Step 8: Microbial Profiling

[wbsimey]

Hello,
I see no other posts for issues or help, so I am not sure this is the proper place to seek help. If not, please direct me to the proper location.

I installed the iMap pipeline on a large Ubuntu system following your iMAP for Unix-Linux environments (in progress). I placed all of my raw reads into iMAP/data/raw. I followed each step and all was going well until I got to Microbial Profiling. I am getting the following errors:

`Linux version

Using Boost,HDF5
mothur v.1.43.0
Last updated: 10/21/19
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

For questions and analysis support, please visit our forum at https://forum.mothur.org

Type 'quit()' to exit program

[NOTE]: Setting random seed to 19760620.

Batch Mode

mothur > set.dir(input=data/mothur/, output=data/mothur/)
Mothur's directories:
outputDir=data/mothur/
inputDir=data/mothur/

mothur > set.current(processors=4)

Using 4 processors.

Current files saved by mothur:
processors=4

Output File Names:
data/mothur/current_files.summary

mothur > align.seqs(fasta=qced.trim.contigs.good.unique.fasta, reference=data/references/silva.seed.align)
Unable to open data/mothur/qced.trim.contigs.good.unique.fasta. Trying input directory data/mothur/qced.trim.contigs.good.unique.fasta.
Unable to open data/mothur/qced.trim.contigs.good.unique.fasta. Trying output directory data/mothur/qced.trim.contigs.good.unique.fasta.
Unable to open data/mothur/qced.trim.contigs.good.unique.fasta. Trying default /home/bsimison/bin/qced.trim.contigs.good.unique.fasta.
Unable to open /home/bsimison/bin/qced.trim.contigs.good.unique.fasta. Trying mothur's executable location /home/bsimison/bin/qced.trim.contigs.good.unique.fasta.
Unable to open /home/bsimison/bin/qced.trim.contigs.good.unique.fasta.
Unable to open data/mothur/qced.trim.contigs.good.unique.fasta

Using 4 processors.
[ERROR]: did not complete align.seqs.

mothur > summary.seqs(fasta=current, count=qced.trim.contigs.good.count_table)
[WARNING]: no file was saved for fasta parameter.
You have no current fasta, summary, contigsreport or alignreport file, one is required.
Unable to open data/mothur/qced.trim.contigs.good.count_table. Trying input directory data/mothur/qced.trim.contigs.good.count_table.
Unable to open data/mothur/qced.trim.contigs.good.count_table. Trying output directory data/mothur/qced.trim.contigs.good.count_table.
Unable to open data/mothur/qced.trim.contigs.good.count_table. Trying default /home/bsimison/bin/qced.trim.contigs.good.count_table.
Unable to open /home/bsimison/bin/qced.trim.contigs.good.count_table. Trying mothur's executable location /home/bsimison/bin/qced.trim.contigs.good.count_table.
Unable to open /home/bsimison/bin/qced.trim.contigs.good.count_table.
Unable to open data/mothur/qced.trim.contigs.good.count_table

Using 4 processors.
[ERROR]: did not complete summary.seqs.

mothur > screen.seqs(fasta=current, count=current, maxambig=0, minlength=200, maxlength=310, maxhomop=8)
[WARNING]: no file was saved for count parameter.
[WARNING]: no file was saved for fasta parameter.
You have no current fastafile and the fasta parameter is required.

Using 4 processors.
[ERROR]: did not complete screen.seqs.

mothur > summary.seqs(fasta=current, count=current)
[WARNING]: no file was saved for count parameter.
[WARNING]: no file was saved for fasta parameter.
You have no current fasta, summary, contigsreport or alignreport file, one is required.

Using 4 processors.
[ERROR]: did not complete summary.seqs.

mothur > filter.seqs(fasta=current, vertical=T)
[WARNING]: no file was saved for fasta parameter.
You have no current fastafile and the fasta parameter is required.

Using 4 processors.
[ERROR]: did not complete filter.seqs.

mothur > summary.seqs(fasta=current, count=current)
[WARNING]: no file was saved for count parameter.
[WARNING]: no file was saved for fasta parameter.
You have no current fasta, summary, contigsreport or alignreport file, one is required.

Using 4 processors.
[ERROR]: did not complete summary.seqs.

mothur > unique.seqs(fasta=current, count=current)
[WARNING]: no file was saved for count parameter.
[WARNING]: no file was saved for fasta parameter.
You have no current fastafile and the fasta parameter is required.
[ERROR]: did not complete unique.seqs.

mothur > summary.seqs(fasta=current, count=current)
[WARNING]: no file was saved for count parameter.
[WARNING]: no file was saved for fasta parameter.
You have no current fasta, summary, contigsreport or alignreport file, one is required.

Using 4 processors.
[ERROR]: did not complete summary.seqs.

mothur > quit()

It took 0 seconds to run 11 commands from code/seqprocessing/02_align_for_16S_consensus.batch batch file.

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Detected 8 [ERROR] messages, please review.

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<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Detected 12 [WARNING] messages, please review.
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
[Error] Sorry, sequence alignment did not complete, exiting...!
(base) bsimison@rosalindf:/iMAP$ cd data/mothur/
(base) bsimison@rosalindf:/iMAP/data/mothur$ lt
total 8.0K`

Any ideas what I am doing wrong?