Notebook

In [1]:

%%bash
echo "TODAY'S DATE:"
date
echo "------------"
echo ""
lsb_release -a
echo ""
echo "------------"
echo "HOSTNAME: "; hostname 
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh

TODAY'S DATE:
Wed Jan  3 15:23:35 PST 2018
------------

Distributor ID:	Ubuntu
Description:	Ubuntu 16.04.3 LTS
Release:	16.04
Codename:	xenial

------------
HOSTNAME: 
emu

------------
Computer Specs:

Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                16
On-line CPU(s) list:   0-15
Thread(s) per core:    2
Core(s) per socket:    4
Socket(s):             2
NUMA node(s):          1
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 26
Model name:            Intel(R) Xeon(R) CPU           E5520  @ 2.27GHz
Stepping:              5
CPU MHz:               2394.000
CPU max MHz:           2394.0000
CPU min MHz:           1596.0000
BogoMIPS:              4521.80
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              8192K
NUMA node0 CPU(s):     0-15
Flags:                 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts nopl xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca sse4_1 sse4_2 popcnt lahf_lm tpr_shadow vnmi flexpriority ept vpid dtherm ida

------------

Memory Specs

              total        used        free      shared  buff/cache   available
Mem:            47G         29G        5.3G        462M         12G         16G
Swap:           11G        6.5G        5.5G

No LSB modules are available.

In [2]:

%%bash
mkdir /home/sam/analyses/20180103_oly_pbjelly

In [3]:

ls /home/sam/analyses/20180103_oly_pbjelly/

In [4]:

%%bash
cp /home/sam/analyses/20171130_oly_pbjelly/Protocol.xml /home/sam/analyses/20180103_oly_pbjelly/

In [5]:

%%bash
cat /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

<jellyProtocol>
    <reference>/home/sam/data/oly_BGI_scaffolds.fasta</reference>  
    <outputDir>/home/sam/analyses/20171130_oly_pbjelly</outputDir>
    <blasr>-minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 20 -maxScore -500 -nproc 48 -noSplitSubreads</blasr>
    <input baseDir="/home/sam/data/">
        <job>m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq</job>
        <job>m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq</job>
	<job>m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq</job>
	<job>m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq</job>
	<job>m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq</job>
	<job>m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq</job>
	<job>m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq</job>
    </input>
</jellyProtocol>

In [6]:

%%bash
sed -i 's/20171130_oly_pbjelly/20180103_oly_pbjelly/g' /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

In [7]:

%%bash
cat /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

<jellyProtocol>
    <reference>/home/sam/data/oly_BGI_scaffolds.fasta</reference>  
    <outputDir>/home/sam/analyses/20171130_oly_pbjelly</outputDir>
    <blasr>-minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 20 -maxScore -500 -nproc 48 -noSplitSubreads</blasr>
    <input baseDir="/home/sam/data/">
        <job>m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq</job>
        <job>m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq</job>
	<job>m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq</job>
	<job>m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq</job>
	<job>m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq</job>
	<job>m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq</job>
	<job>m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq</job>
    </input>
</jellyProtocol>

WHOOPS! Copy/paste error. Let's try again...

In [8]:

%%bash
cat /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

<jellyProtocol>
    <reference>/home/sam/data/oly_BGI_scaffolds.fasta</reference>  
    <outputDir>/home/sam/analyses/20180103_oly_pbjelly</outputDir>
    <blasr>-minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 20 -maxScore -500 -nproc 48 -noSplitSubreads</blasr>
    <input baseDir="/home/sam/data/">
        <job>m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq</job>
        <job>m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq</job>
	<job>m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq</job>
	<job>m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq</job>
	<job>m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq</job>
	<job>m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq</job>
	<job>m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq</job>
    </input>
</jellyProtocol>

Need to insert special command to tell PB Jelly that this is NOT on a cluster. Will insert into line #4 of `Protocol.xml` file using `sed`¶

Hopefully this adjustment will increase the speed of PB Jelly on Emu.

In [9]:

%%bash
sed -i '4i    <command>${CMD} ${JOBNAME} 2> ${STDERR} 1> ${STDOUT} &</command>' /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

In [10]:

%%bash
cat /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

<jellyProtocol>
    <reference>/home/sam/data/oly_BGI_scaffolds.fasta</reference>  
    <outputDir>/home/sam/analyses/20180103_oly_pbjelly</outputDir>
<command>${CMD} ${JOBNAME} 2> ${STDERR} 1> ${STDOUT} &</command>
    <blasr>-minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 20 -maxScore -500 -nproc 48 -noSplitSubreads</blasr>
    <input baseDir="/home/sam/data/">
        <job>m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq</job>
        <job>m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq</job>
	<job>m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq</job>
	<job>m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq</job>
	<job>m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq</job>
	<job>m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq</job>
	<job>m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq</job>
    </input>
</jellyProtocol>

In [11]:

%%bash
source /home/shared/PBSuite_15.8.24/setup.sh
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

2018-01-03 15:37:24,992 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

2018-01-03 15:37:24,993 [ERROR] If you're actually sure the input Protocol is where you said it is, then the Protocol doesn't have valid XML Format. Use an XML validator.

real	0m0.370s
user	0m0.244s
sys	0m0.900s
2018-01-03 15:37:25,140 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

2018-01-03 15:37:25,141 [ERROR] If you're actually sure the input Protocol is where you said it is, then the Protocol doesn't have valid XML Format. Use an XML validator.

real	0m0.152s
user	0m0.288s
sys	0m1.064s
2018-01-03 15:37:25,314 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

2018-01-03 15:37:25,316 [ERROR] If you're actually sure the input Protocol is where you said it is, then the Protocol doesn't have valid XML Format. Use an XML validator.

real	0m0.177s
user	0m0.308s
sys	0m1.264s
2018-01-03 15:37:25,467 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

2018-01-03 15:37:25,469 [ERROR] If you're actually sure the input Protocol is where you said it is, then the Protocol doesn't have valid XML Format. Use an XML validator.

real	0m0.155s
user	0m0.208s
sys	0m0.628s
2018-01-03 15:37:25,689 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

2018-01-03 15:37:25,690 [ERROR] If you're actually sure the input Protocol is where you said it is, then the Protocol doesn't have valid XML Format. Use an XML validator.

real	0m0.217s
user	0m0.312s
sys	0m1.268s
2018-01-03 15:37:25,832 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

2018-01-03 15:37:25,834 [ERROR] If you're actually sure the input Protocol is where you said it is, then the Protocol doesn't have valid XML Format. Use an XML validator.

real	0m0.139s
user	0m0.164s
sys	0m0.568s

In [12]:

%%bash
source ~/.bashrc
source ~/.bash_aliases
emailme

bash: line 3: emailme: command not found

Fixed spacing of newly inserted line.¶

In [13]:

%%bash
cat /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

<jellyProtocol>
    <reference>/home/sam/data/oly_BGI_scaffolds.fasta</reference>  
    <outputDir>/home/sam/analyses/20180103_oly_pbjelly</outputDir>
    <command>${CMD} ${JOBNAME} 2> ${STDERR} 1> ${STDOUT} &</command>
    <blasr>-minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 20 -maxScore -500 -nproc 48 -noSplitSubreads</blasr>
    <input baseDir="/home/sam/data/">
        <job>m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq</job>
        <job>m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq</job>
	<job>m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq</job>
	<job>m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq</job>
	<job>m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq</job>
	<job>m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq</job>
	<job>m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq</job>
    </input>
</jellyProtocol>

In [14]:

%%bash
source /home/shared/PBSuite_15.8.24/setup.sh
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

2018-01-03 15:42:50,796 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

2018-01-03 15:42:50,798 [ERROR] If you're actually sure the input Protocol is where you said it is, then the Protocol doesn't have valid XML Format. Use an XML validator.

real	0m0.177s
user	0m0.292s
sys	0m1.220s
2018-01-03 15:42:50,947 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

2018-01-03 15:42:50,949 [ERROR] If you're actually sure the input Protocol is where you said it is, then the Protocol doesn't have valid XML Format. Use an XML validator.

real	0m0.152s
user	0m0.284s
sys	0m1.052s
2018-01-03 15:42:51,081 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

2018-01-03 15:42:51,082 [ERROR] If you're actually sure the input Protocol is where you said it is, then the Protocol doesn't have valid XML Format. Use an XML validator.

real	0m0.127s
user	0m0.136s
sys	0m0.592s
2018-01-03 15:42:51,208 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

2018-01-03 15:42:51,209 [ERROR] If you're actually sure the input Protocol is where you said it is, then the Protocol doesn't have valid XML Format. Use an XML validator.

real	0m0.129s
user	0m0.204s
sys	0m0.692s
2018-01-03 15:42:51,359 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

2018-01-03 15:42:51,360 [ERROR] If you're actually sure the input Protocol is where you said it is, then the Protocol doesn't have valid XML Format. Use an XML validator.

real	0m0.153s
user	0m0.260s
sys	0m1.084s
2018-01-03 15:42:51,496 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

2018-01-03 15:42:51,498 [ERROR] If you're actually sure the input Protocol is where you said it is, then the Protocol doesn't have valid XML Format. Use an XML validator.

real	0m0.139s
user	0m0.256s
sys	0m0.768s

In [15]:

%%bash
sed -i 's/\&/\&amp;/g' /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

In [16]:

%%bash
cat /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

<jellyProtocol>
    <reference>/home/sam/data/oly_BGI_scaffolds.fasta</reference>  
    <outputDir>/home/sam/analyses/20180103_oly_pbjelly</outputDir>
    <command>${CMD} ${JOBNAME} 2> ${STDERR} 1> ${STDOUT} &amp;</command>
    <blasr>-minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 20 -maxScore -500 -nproc 48 -noSplitSubreads</blasr>
    <input baseDir="/home/sam/data/">
        <job>m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq</job>
        <job>m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq</job>
	<job>m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq</job>
	<job>m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq</job>
	<job>m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq</job>
	<job>m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq</job>
	<job>m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq</job>
	<job>m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq</job>
    </input>
</jellyProtocol>

In [ ]:

%%bash
source /home/shared/PBSuite_15.8.24/setup.sh
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml
time python /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20180103_oly_pbjelly/Protocol.xml

In [ ]:

%%bash
source ~/.bashrc
source ~/.bash_aliases
emailme

In [ ]:

Need to insert special command to tell PB Jelly that this is NOT on a cluster. Will insert into line #4 of Protocol.xml file using sed¶

Fixed spacing of newly inserted line.¶

Need to insert special command to tell PB Jelly that this is NOT on a cluster. Will insert into line #4 of `Protocol.xml` file using `sed`¶