Error: sh: 1: -ufactor=1000: not found

Run command:

python /share/shannon/shannon.py -k25 -p 60 \
-o /mnt/data3/macmanes/error/shannon/shannon20Mk25 \
--left $RAID/error/rcorr20M/20.subsamp_1.cor.fq \
--right $RAID/error/rcorr20M/20.subsamp_2.cor.fq

This is strange, because the 1st gpmetis command worked, but not the second.. This package is def. in my $PATH as well:

$which gpmetis
/usr/bin/gpmetis

the stdout, with error:

--------------------------------------------
Shannon: RNA Seq de novo Assembly
--------------------------------------------
Checking the various dependencies
--------------------------------------------
Using jellyfish in /share/quorum/bin/jellyfish
Using GPMETIS in /usr/bin/gpmetis
--------------------------------------------
Wed Feb 10 09:08:22 2016: Starting Shannon run..
Using Quorum in /share/quorum/bin/quorum
Using GNU Parallel in /usr/bin/parallel
Wed Feb 10 09:08:22 2016: Running Quorum for read error correction with quality scores..
Wed Feb 10 09:31:28 2016: Starting Jellyfish to extract Kmers from Reads..
Wed Feb 10 09:32:49 2016: Jellyfish finished..
Wed Feb 10 09:32:49 2016: Starting Kmer error correction..
Wed Feb 10 09:33:28 2016: Loading, processed 1000000
...
Wed Feb 10 11:41:25 2016: Correction, processed 137000000
Wed Feb 10 11:42:49 2016: 137863768 K-mers remaining after error correction.
Wed Feb 10 12:08:49 2016: Creating Kmers from (K+1)-mers..
Wed Feb 10 12:14:49 2016: 137863768 K+1-mers loaded.
Wed Feb 10 12:20:27 2016: 137812539 K-mers produced.
gpmetis -ufactor=1000 /mnt/data3/macmanes/error/shannon/shannon20Mk25/component1.txt 100
******************************************************************************
METIS 5.0 Copyright 1998-13, Regents of the University of Minnesota
 (HEAD: , Built on: Jul 20 2013, 23:18:43)
 size of idx_t: 32bits, real_t: 32bits, idx_t *: 64bits

Graph Information -----------------------------------------------------------
 Name: /mnt/data3/macmanes/error/shannon/shannon20Mk25/component1.txt, #Vertices: 308394, #Edges: 573390, #Parts: 100

Options ---------------------------------------------------------------------
 ptype=kway, objtype=cut, ctype=shem, rtype=greedy, iptype=metisrb
 dbglvl=0, ufactor=2.000, no2hop=NO, minconn=NO, contig=NO, nooutput=NO
 seed=-1, niter=10, ncuts=1

Direct k-way Partitioning ---------------------------------------------------
 - Edgecut: 105916, communication volume: 148626.

 - Balance:
     constraint #0:  2.000 out of 0.000

 - Most overweight partition:
     pid: 17, actual: 6168, desired: 3083, ratio: 2.00.

 - Subdomain connectivity: max: 99, min: 52, avg: 86.80

 - There are 96 non-contiguous partitions.
   Total components after removing the cut edges: 660,
   max components: 30 for pid: 47.

Timing Information ----------------------------------------------------------
  I/O:                             0.153 sec
  Partitioning:                    1.130 sec   (METIS time)
  Reporting:                       0.083 sec

Memory Information ----------------------------------------------------------
  Max memory used:                39.662 MB
******************************************************************************
Wed Feb 10 12:49:27 2016: gpmetis for partitioning 1 is complete -- Component 0: 100 partitions,
r
Wed Feb 10 12:57:41 2016: k1mers2component dictionary created
Wed Feb 10 13:31:13 2016: reads partititoned
...
Wed Feb 10 14:30:44 2016: k1mer Streaming, processed 137000000
Wed Feb 10 14:31:06 2016: k1mers weights stored in dictionary
Wed Feb 10 14:36:22 2016: k1mers written to file
Wed Feb 10 14:44:35 2016: kmers2component dictionary created
Wed Feb 10 14:44:58 2016: kmer Streaming, processed 1000000
...
Wed Feb 10 15:38:07 2016: kmer Streaming, processed 137000000
Wed Feb 10 15:38:26 2016: kmers weights stored in dictionary
Wed Feb 10 15:43:05 2016: kmers written to file
 -ufactor=1000 /mnt/data3/macmanes/error/shannon/shannon20Mk25/component1r2.txt 100
sh: 1: -ufactor=1000: not found
Wed Feb 10 15:44:22 2016: gpmetis for partitioning 2 is complete -- Component 0: 100 partitions,
Traceback (most recent call last):
  File "/share/shannon/shannon.py", line 317, in <module>
    [r2_components_broken, r2_new_components] = kmers_for_component(kmer_directory, reads_files, base_directory_name, r1_contig_file_extension, r2_new_kmer_tag, r2_graph_file_extens
ion, get_og_comp_kmers, get_partition_kmers, double_stranded, paired_end, True, partition_size, overload, K)
  File "/share/shannon/kmers_for_component.py", line 96, in kmers_for_component
    with open(directory_name+"/component" + str(i+1) + graph_file_extension + ".part." + str(components_broken[i]) , 'r') as f_component:
IOError: [Errno 2] No such file or directory: '/mnt/data3/macmanes/error/shannon/shannon20Mk25/component1r2.txt.part.100'

sreeramkannan / Shannon

Error: sh: 1: -ufactor=1000: not found #5