Comments on: Introducing PAPRICA

By: Jeff

Jeff — Thu, 23 Mar 2017 19:28:05 +0000

In reply to Daniel. I’m replying to you via email to keep the comment thread clean. You seem to have paprica installed in a very odd location which could be part of the problem. I recommend cloning the repository to your home directory. Try that and let me know if the problem persists.

By: Daniel

Daniel — Thu, 23 Mar 2017 17:55:54 +0000

In reply to Jeff.

Hi Jeff,
The error persist. I am receiving the following.
Could you help me with that, please?

./paprica-run.sh test.bacteria bacteria
# cmalign :: align sequences to a CM
# INFERNAL 1.1.2 (July 2016)
# Copyright (C) 2016 Howard Hughes Medical Institute.
# Freely distributed under a BSD open source license.
# – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
# CM file: /usr/local/install/temp/paprica-paprica_v0.4.0a/models/bacteria_ssu.cm
# sequence file: /usr/local/install/temp/paprica-paprica_v0.4.0a/test.bacteria.clean.fasta
# CM name: SSU_rRNA_bacteria
# saving alignment to file: /usr/local/install/temp/paprica-paprica_v0.4.0a/test.bacteria.clean.align.sto
# output alignment format specified as: Pfam
# output alignment alphabet: DNA
# number of worker threads: 64
# – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –
# running time (s)
# ——————————-
# idx seq name length cm from cm to trunc bit sc avg pp band calc alignment total mem (Mb)
# — ————– —— ——- ——- —– ——– —— ——— ——— ——— ——–
1 SRR953432.50 84 968 1054 3′ 39.93 0.974 0.08 0.30 0.38 2.91
2 SRR953432.90 84 968 1054 3′ 39.93 0.974 0.06 0.21 0.27 2.91
3 SRR953432.97 84 968 1054 3′ 39.93 0.974 0.09 0.29 0.37 2.91
4 SRR953432.307 84 968 1054 3′ 39.93 0.974 0.08 0.30 0.38 2.91
5 SRR953432.386 84 968 1054 3′ 39.93 0.974 0.08 0.29 0.37 2.91
6 SRR953432.641 84 968 1054 3′ 39.93 0.974 0.07 0.30 0.38 2.91
7 SRR953432.836 84 968 1054 3′ 39.93 0.974 0.08 0.29 0.38 2.91
8 SRR953432.860 84 968 1054 3′ 39.93 0.974 0.07 0.30 0.37 2.91
9 SRR953432.903 84 968 1054 3′ 39.93 0.974 0.08 0.30 0.38 2.91
10 SRR953432.1226 84 968 1054 3′ 39.93 0.974 0.07 0.29 0.36 2.91
11 SRR953432.1336 84 968 1054 3′ 39.93 0.974 0.07 0.30 0.37 2.91
12 SRR953432.1341 84 968 1054 3′ 39.93 0.974 0.09 0.27 0.36 2.91
13 SRR953432.1426 84 968 1054 3′ 39.93 0.974 0.09 0.27 0.36 2.91
14 SRR953432.1527 84 968 1054 3′ 39.93 0.974 0.07 0.28 0.35 2.91
15 SRR953432.1647 84 968 1054 3′ 39.93 0.974 0.09 0.27 0.36 2.91
16 SRR953432.2076 84 968 1054 3′ 39.93 0.974 0.07 0.30 0.37 2.91
17 SRR953432.2160 84 968 1054 3′ 39.93 0.974 0.07 0.31 0.38 2.91
18 SRR953432.2164 84 968 1054 3′ 39.93 0.974 0.07 0.30 0.36 2.91
19 SRR953432.2192 84 968 1054 3′ 39.93 0.974 0.07 0.30 0.37 2.91
20 SRR953432.2374 84 968 1054 3′ 39.93 0.974 0.07 0.29 0.36 2.91
21 SRR953432.2713 84 968 1054 3′ 39.93 0.974 0.09 0.28 0.37 2.91
22 SRR953432.2934 84 968 1054 3′ 39.93 0.974 0.09 0.28 0.37 2.91
23 SRR953432.3261 84 968 1054 3′ 39.93 0.974 0.07 0.31 0.37 2.91
24 SRR953432.3998 84 968 1054 3′ 39.93 0.974 0.09 0.29 0.37 2.91
25 SRR953432.4090 84 968 1054 3′ 39.93 0.974 0.07 0.30 0.37 2.91
26 SRR953432.4248 84 968 1054 3′ 39.93 0.974 0.07 0.29 0.36 2.91
27 SRR953432.4378 84 968 1054 3′ 39.93 0.974 0.07 0.28 0.36 2.91
28 SRR953432.4573 84 968 1054 3′ 39.93 0.974 0.07 0.31 0.38 2.91
#
# CPU time: 4.63u 2.63s 00:00:07.26 Elapsed: 00:00:01.58
# Saving alignment to file /usr/local/install/temp/paprica-paprica_v0.4.0a/test.bacteria.combined_16S.bacteria.tax.clean.align.sto … done
#
# CPU time: 0.11u 0.03s 00:00:00.14 Elapsed: 00:00:00.15
Running pplacer v1.1.alpha19-0-g807f6f3 analysis on /usr/local/install/temp/paprica-paprica_v0.4.0a/test.bacteria.combined_16S.bacteria.tax.clean.align.fasta…
Found reference sequences in given alignment file. Using those for reference alignment.
Pre-masking sequences… sequence length cut from 2630 to 84.
Note: you have 84 sites after pre-masking. That means there is rather little information in these sequences for placement.
Determining figs… figs disabled.
Allocating memory for internal nodes… done.
Caching likelihood information on reference tree… done.
Pulling exponents… done.
Preparing the edges for baseball… done.
working on SRR953432.4573 (1/1)…
Traceback (most recent call last):
File “/usr/local/bin/paprica-tally_pathways.py”, line 117, in
genome_data = pd.DataFrame.from_csv(ref_dir_domain + ‘genome_data.final.csv’, header = 0, index_col = 0)
File “/usr/lib64/python2.7/site-packages/pandas/core/frame.py”, line 1177, in from_csv
infer_datetime_format=infer_datetime_format)
File “/usr/lib64/python2.7/site-packages/pandas/io/parsers.py”, line 498, in parser_f
return _read(filepath_or_buffer, kwds)
File “/usr/lib64/python2.7/site-packages/pandas/io/parsers.py”, line 275, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File “/usr/lib64/python2.7/site-packages/pandas/io/parsers.py”, line 590, in __init__
self._make_engine(self.engine)
File “/usr/lib64/python2.7/site-packages/pandas/io/parsers.py”, line 731, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File “/usr/lib64/python2.7/site-packages/pandas/io/parsers.py”, line 1103, in __init__
self._reader = _parser.TextReader(src, **kwds)
File “pandas/parser.pyx”, line 353, in pandas.parser.TextReader.__cinit__ (pandas/parser.c:3246)
File “pandas/parser.pyx”, line 591, in pandas.parser.TextReader._setup_parser_source (pandas/parser.c:6111)
IOError: File /usr/local/bin/ref_genome_database/bacteria/genome_data.final.csv does not exist

By: Jeff

Jeff — Fri, 17 Mar 2017 20:41:55 +0000

In reply to Daniel. Daniel, I think I found the bug - change line 52 in paprica-tally_pathways.py to: paprica_path = os.path.dirname(os.path.abspath("__file__")) + '/' Alternatively reclone from the repository as that version should be up to date. Let me know if still having problems.

By: Daniel

Daniel — Fri, 17 Mar 2017 18:02:31 +0000

Hi
I am having problems with paprica’s execution, I am reciving the following erro messenger in pandas as follow

Traceback (most recent call last):
File “/usr/local/bin/paprica-tally_pathways.py”, line 117, in
genome_data = pd.DataFrame.from_csv(ref_dir_domain + ‘genome_data.final.csv’, header = 0, index_col = 0)
File “/usr/lib64/python2.7/site-packages/pandas/core/frame.py”, line 1177, in from_csv
infer_datetime_format=infer_datetime_format)
File “/usr/lib64/python2.7/site-packages/pandas/io/parsers.py”, line 498, in parser_f
return _read(filepath_or_buffer, kwds)
File “/usr/lib64/python2.7/site-packages/pandas/io/parsers.py”, line 275, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File “/usr/lib64/python2.7/site-packages/pandas/io/parsers.py”, line 590, in __init__
self._make_engine(self.engine)
File “/usr/lib64/python2.7/site-packages/pandas/io/parsers.py”, line 731, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File “/usr/lib64/python2.7/site-packages/pandas/io/parsers.py”, line 1103, in __init__
self._reader = _parser.TextReader(src, **kwds)
File “pandas/parser.pyx”, line 353, in pandas.parser.TextReader.__cinit__ (pandas/parser.c:3246)
File “pandas/parser.pyx”, line 591, in pandas.parser.TextReader._setup_parser_source (pandas/parser.c:6111)
IOError: File /usr/local/bin/ref_genome_database/bacteria/genome_data.final.csv does not exist

By: Roman

Roman — Mon, 17 Oct 2016 11:31:25 +0000

In reply to Jeff. Thanks Jeff, it is great ...

By: Jeff

Jeff — Fri, 14 Oct 2016 06:39:48 +0000

In reply to Roman. Roman, great question, I should make that more clear in the documentation. The copy number correction is applied automatically to enzymes and pathways. You will notice that the total number for each enzyme or pathway is often not an integer as a result.

By: Roman

Roman — Thu, 13 Oct 2016 13:03:27 +0000

Dear Jeff,
May I ask you, how does Paprica handle 16S rRNA copy number?
I can read in the text “… number of 16S rRNA gene copies associated with each 16S rRNA gene …“ does it mean that 16S rRNA gene copies are taken into account when computing abundance of pathways/enzymes or should it be corrected explicitly/subsequently by user/me?

I would like to thank you for a great piece of software, it is wonderful work.

By: Jeff

Jeff — Thu, 29 Oct 2015 22:13:48 +0000

Aneesha,
Thanks for giving paprica a try. You’ll receive an email from me shortly with some troubleshooting instructions.

-Jeff

By: aneesha

aneesha — Thu, 29 Oct 2015 15:10:46 +0000

I have cloned the genome_finder repositiory from git and am trying to run paprica_run.sh on a Fasta file of representative OTU sequences from human microbiome, with the following error. Please let me know a work through.

MacQIIME*****-MacBook-Air:genome_finder $ paprica_run.sh /Users/*****/Desktop/Saliva_rep_set
cat: /Users/****/genome_finder/genome_finder/ref_genome_database/combined_16S.tax.refpkg/combined_16S.tax.clean.align.fasta: No such file or directory
/bin/bash: seqmagick: command not found
Failed to parse command line: No such option “–outformat”.
Usage: cmalign [-options]
Usage: cmalign [-options] –merge

The –merge option merges the two alignments in and
created by previous runs of cmalign with into a single alignment.
To see more help on available options, do cmalign -h

/bin/bash: seqmagick: command not found
/bin/bash: seqmagick: command not found
Uncaught exception: Sys_error(“/Users/*****/genome_finder/genome_finder/ref_genome_database/combined_16S.tax.refpkg: No such file or directory”)
Running pplacer v1.1.alpha13r2-0-g79a8847 analysis on /Users/*****/Desktop/Saliva_rep_set.combined_16S.tax.clean.align.fasta…
Fatal error: exception Sys_error(“/*****/aneesha/genome_finder/genome_finder/ref_genome_database/combined_16S.tax.refpkg: No such file or directory”)
Uncaught exception: Sys_error(“/Users/*****/Desktop/Saliva_rep_set.combined_16S.tax.clean.align.jplace: No such file or directory”)
Fatal error: exception Sys_error(“/Users/*****/Desktop/Saliva_rep_set.combined_16S.tax.clean.align.jplace: No such file or directory”)
Uncaught exception: Sys_error(“/Users/*****/Desktop/Saliva_rep_set.combined_16S.tax.clean.align.jplace: No such file or directory”)
Fatal error: exception Sys_error(“/Users/*****/Desktop/Saliva_rep_set.combined_16S.tax.clean.align.jplace: No such file or directory”)
Traceback (most recent call last):
File “paprica_tally_pathways_v0.20.py”, line 49, in
genome_data = pd.DataFrame.from_csv(variables[‘ref_dir’] + ‘genome_data.final.csv’, header = 0, index_col = 0)
File “/macqiime/anaconda/lib/python2.7/site-packages/pandas/core/frame.py”, line 1036, in from_csv
infer_datetime_format=infer_datetime_format)
File “/macqiime/anaconda/lib/python2.7/site-packages/pandas/io/parsers.py”, line 474, in parser_f
return _read(filepath_or_buffer, kwds)
File “/macqiime/anaconda/lib/python2.7/site-packages/pandas/io/parsers.py”, line 250, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File “/macqiime/anaconda/lib/python2.7/site-packages/pandas/io/parsers.py”, line 566, in __init__
self._make_engine(self.engine)
File “/macqiime/anaconda/lib/python2.7/site-packages/pandas/io/parsers.py”, line 705, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File “/macqiime/anaconda/lib/python2.7/site-packages/pandas/io/parsers.py”, line 1072, in __init__
self._reader = _parser.TextReader(src, **kwds)
File “pandas/parser.pyx”, line 350, in pandas.parser.TextReader.__cinit__ (pandas/parser.c:3173)
File “pandas/parser.pyx”, line 594, in pandas.parser.TextReader._setup_parser_source (pandas/parser.c:5912)
IOError: File /Users/*****/genome_finder/genome_finder/ref_genome_database/genome_data.final.csv does not exist