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
Tue Nov 14 06:57:22 PST 2017
------------

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        6.4G         21G        504M         18G         39G
Swap:           11G        4.3G        7.7G

No LSB modules are available.

In [2]:

%%bash
pwd
ls -lh

/home/sam/data
total 96G
-rw-rw-r-- 1 sam sam 6.6G Oct 24 14:48 151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz
-rw-rw-r-- 1 sam sam 6.9G Oct 24 14:49 151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz
-rw-rw-r-- 1 sam sam 6.6G Oct 24 14:50 151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz
-rw-rw-r-- 1 sam sam 6.8G Oct 24 14:52 151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz
-rw-rw-r-- 1 sam sam 3.8G Oct 24 14:53 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz
-rw-rw-r-- 1 sam sam 4.0G Oct 24 14:54 151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz
-rw-rw-r-- 1 sam sam 2.4G Oct 24 14:54 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz
-rw-rw-r-- 1 sam sam 2.8G Oct 24 14:55 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz
-rw-rw-r-- 1 sam sam 1.3G Oct 24 14:55 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz
-rw-rw-r-- 1 sam sam 1.5G Oct 24 14:56 160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz
-rw-rw-r-- 1 sam sam 2.4G Oct 24 14:56 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz
-rw-rw-r-- 1 sam sam 2.8G Oct 24 14:57 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz
-rw-rw-r-- 1 sam sam 1.3G Oct 24 14:57 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz
-rw-rw-r-- 1 sam sam 1.5G Oct 24 14:57 160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz
-rw-rw-r-- 1 sam sam 2.7G Oct 24 14:58 160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz
-rw-rw-r-- 1 sam sam 3.1G Oct 24 14:58 160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz
-rw-rw-r-- 1 sam sam 2.6G Oct 24 14:59 160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz
-rw-rw-r-- 1 sam sam 3.0G Oct 24 15:00 160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz
-rw-rw-r-- 1 sam sam  33K Nov 14 06:52 2017113_emu_pbjelly_22mer_plat.ipynb
-rw-rw-r-- 1 sam sam  33K Nov 14 06:53 201711_emu_pbjelly_BGI_scaffold.ipynb
-rw-rw-r-- 1 sam sam 372M Oct 24 15:02 m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq
-rwxrwxr-x 1 sam sam 2.7G Oct 24 15:02 m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq
-rwxrwxr-x 1 sam sam 3.0G Oct 24 15:02 m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq
-rwxrwxr-x 1 sam sam 2.7G Oct 24 15:02 m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq
-rwxrwxr-x 1 sam sam 3.0G Oct 24 15:03 m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq
-rwxrwxr-x 1 sam sam 2.8G Oct 24 15:03 m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq
-rwxrwxr-x 1 sam sam 2.8G Oct 24 15:03 m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq
-rwxrwxr-x 1 sam sam 2.0G Oct 24 15:04 m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq
-rwxrwxr-x 1 sam sam 1.8G Oct 24 15:04 m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq
-rwxrwxr-x 1 sam sam 1.6G Oct 24 15:04 m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq
-rwxrwxr-x 1 sam sam 1.8G Oct 24 15:04 m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq
-rw-rw-r-- 1 sam sam 2.0G Nov 13 16:33 oly_plat_22mer_sb_contig.fasta
-rw-rw-r-- 1 sam sam 1.9G Nov 13 16:04 oly_plat_22mer_sb_contig.fasta.original
-rw-rw-r-- 1 sam sam 6.2G Nov 13 16:57 oly_plat_22mer_sb_contig.fasta.sa
-rw-rw-r-- 1 sam sam 690M Nov 13 16:33 oly_plat_22mer_sb_contig.gapInfo.bed
-rw-rw-r-- 1 sam sam  387 Nov 13 16:57 setup.err
-rw-rw-r-- 1 sam sam    0 Nov 13 16:23 setup.out

Need reference assembly of Illumina data.¶

Copy BGI scaffolded assembly and rename to something more descriptive.

In [3]:

%%bash
time cp /mnt/owl/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/Ostrea_lurida.fa oly_BGI_scaffolds.fasta
ls -lh oly_BGI_scaffolds.fasta

-rw-rw-r-- 1 sam sam 762M Nov 14 07:00 oly_BGI_scaffolds.fasta

real	0m10.889s
user	0m0.008s
sys	0m0.888s

In [4]:

%%bash
mkdir /home/sam/analyses/2017111_oly_pbjelly

In [5]:

ls /home/sam/analyses/20171113_oly_pbjelly/

assembly/            mapping/    output.out    support/
gap_fill_status.txt  output.err  Protocol.xml

In [6]:

ls /home/sam/analyses/2017111_oly_pbjelly

In [7]:

mv /home/sam/analyses/2017111_oly_pbjelly /home/sam/analyses/20171114_oly_pbjelly

In [8]:

ls /home/sam/analyses/20171114_oly_pbjelly/

View the Protocol.xml file tha PB Jelly uses to run.¶

In [9]:

cat /home/sam/analyses/20171114_oly_pbjelly/Protocol.xml

<jellyProtocol>
    <reference>/home/sam/data/oly_BGI_scaffolds.fasta</reference>  
    <outputDir>/home/sam/analyses/20171114_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>

Source (i.e. load) the PB Jelly setup script and run PB Jelly.¶

PB Jelly has 5 steps that must be run sequentially:¶

setup
mapping
support
extraction
assembly
output

In [10]:

%%bash
source /home/shared/PBSuite_15.8.24/setup.sh
python /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20171113_oly_pbjelly/Protocol.xml
python /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20171113_oly_pbjelly/Protocol.xml
python /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20171113_oly_pbjelly/Protocol.xml
python /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20171113_oly_pbjelly/Protocol.xml
python /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20171113_oly_pbjelly/Protocol.xml
python /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20171113_oly_pbjelly/Protocol.xml

2017-11-14 07:06:41,980 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20171113_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.

[WARNING] Couldn't find /home/sam/data/oly_plat_22mer_sb_contig.qual... assuming there isn't a quality file for the reference
2017-11-14 07:06:41,994 [INFO] Executing Stage: setup
2017-11-14 07:41:26,277 [INFO] Finished Running Stage: setup
2017-11-14 07:41:27,495 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20171113_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.

[WARNING] Couldn't find /home/sam/data/oly_plat_22mer_sb_contig.qual... assuming there isn't a quality file for the reference
2017-11-14 07:41:27,554 [INFO] Executing Stage: mapping
2017-11-14 07:41:27,554 [INFO] Running blasr
2017-11-14 07:41:28,937 [INFO] Finished Running Stage: mapping
2017-11-14 07:41:29,101 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20171113_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.

[WARNING] Couldn't find /home/sam/data/oly_plat_22mer_sb_contig.qual... assuming there isn't a quality file for the reference
2017-11-14 07:41:29,103 [INFO] Executing Stage: support
2017-11-14 07:41:29,104 [WARNING] No mapping files found!
2017-11-14 07:41:29,104 [INFO] Finished Running Stage: support
2017-11-14 07:41:29,231 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20171113_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.

[WARNING] Couldn't find /home/sam/data/oly_plat_22mer_sb_contig.qual... assuming there isn't a quality file for the reference
2017-11-14 07:41:29,233 [INFO] Executing Stage: extraction
2017-11-14 08:01:05,256 [INFO] Finished Running Stage: extraction
2017-11-14 08:01:45,356 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20171113_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.

[WARNING] Couldn't find /home/sam/data/oly_plat_22mer_sb_contig.qual... assuming there isn't a quality file for the reference
2017-11-14 08:01:45,593 [INFO] Executing Stage: assembly
2017-11-14 08:04:55,851 [WARNING] No gaps to be assembled were found in /home/sam/analyses/20171113_oly_pbjelly/assembly! Have you run 'extraction' yet?
2017-11-14 08:06:07,253 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20171113_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.

[WARNING] Couldn't find /home/sam/data/oly_plat_22mer_sb_contig.qual... assuming there isn't a quality file for the reference
2017-11-14 08:06:07,254 [INFO] Executing Stage: output
2017-11-14 08:14:39,847 [INFO] Finished Running Stage: output

In [11]:

ls /home/sam/analyses/20171114_oly_pbjelly/

Protocol.xml

Doh! Copy and paste error in PB Jelly command cell above! Used wrong Protocol.xml file. Fixed path below.

In [12]:

%%bash
source /home/shared/PBSuite_15.8.24/setup.sh
python /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20171114_oly_pbjelly/Protocol.xml
python /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20171114_oly_pbjelly/Protocol.xml
python /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20171114_oly_pbjelly/Protocol.xml
python /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20171114_oly_pbjelly/Protocol.xml
python /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20171114_oly_pbjelly/Protocol.xml
python /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20171114_oly_pbjelly/Protocol.xml

2017-11-14 09:27:41,063 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py setup /home/sam/analyses/20171114_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.

[WARNING] Couldn't find /home/sam/data/oly_BGI_scaffolds.qual... assuming there isn't a quality file for the reference
2017-11-14 09:27:41,094 [INFO] Executing Stage: setup
2017-11-14 09:35:52,014 [INFO] Finished Running Stage: setup
2017-11-14 09:35:52,166 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py mapping /home/sam/analyses/20171114_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.

[WARNING] Couldn't find /home/sam/data/oly_BGI_scaffolds.qual... assuming there isn't a quality file for the reference
2017-11-14 09:35:52,169 [INFO] Executing Stage: mapping
2017-11-14 09:35:52,184 [INFO] Running blasr
2017-11-14 09:35:53,836 [INFO] Finished Running Stage: mapping
2017-11-14 09:35:53,991 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py support /home/sam/analyses/20171114_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.

[WARNING] Couldn't find /home/sam/data/oly_BGI_scaffolds.qual... assuming there isn't a quality file for the reference
2017-11-14 09:35:53,993 [INFO] Executing Stage: support
2017-11-14 09:35:53,994 [WARNING] No mapping files found!
2017-11-14 09:35:53,994 [INFO] Finished Running Stage: support
2017-11-14 09:35:54,123 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py extraction /home/sam/analyses/20171114_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.

[WARNING] Couldn't find /home/sam/data/oly_BGI_scaffolds.qual... assuming there isn't a quality file for the reference
2017-11-14 09:35:54,124 [INFO] Executing Stage: extraction
2017-11-14 09:41:23,941 [INFO] Finished Running Stage: extraction
2017-11-14 09:41:24,239 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py assembly /home/sam/analyses/20171114_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.

[WARNING] Couldn't find /home/sam/data/oly_BGI_scaffolds.qual... assuming there isn't a quality file for the reference
2017-11-14 09:41:24,261 [INFO] Executing Stage: assembly
2017-11-14 09:41:32,199 [WARNING] No gaps to be assembled were found in /home/sam/analyses/20171114_oly_pbjelly/assembly! Have you run 'extraction' yet?
2017-11-14 09:41:34,555 [INFO] Running /home/shared/PBSuite_15.8.24/bin/Jelly.py output /home/sam/analyses/20171114_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.

[WARNING] Couldn't find /home/sam/data/oly_BGI_scaffolds.qual... assuming there isn't a quality file for the reference
2017-11-14 09:41:34,557 [INFO] Executing Stage: output
2017-11-14 09:59:51,450 [INFO] Finished Running Stage: output

In [13]:

ls /home/sam/analyses/20171114_oly_pbjelly/

assembly/            jelly.out.qual      output.err    support/
gap_fill_status.txt  liftOverTable.json  output.out
jelly.out.fasta      mapping/            Protocol.xml

In [14]:

%%bash
head /home/sam/analyses/20171114_oly_pbjelly/output.err

[WARNING] Couldn't find /home/sam/data/oly_BGI_scaffolds.qual... assuming there isn't a quality file for the reference
2017-11-14 09:41:34,844 [INFO] Running /home/shared/PBSuite_15.8.24//bin//Collection.py /home/sam/analyses/20171114_oly_pbjelly/Protocol.xml
2017-11-14 09:41:34,844 [INFO] Grabbing Filling Metrics
2017-11-14 09:41:34,845 [INFO] Number of Gaps Addressed 0
2017-11-14 09:41:34,845 [INFO] No Filling Metrics 0
2017-11-14 09:41:34,845 [INFO] Min Read Failed 0
2017-11-14 09:41:34,845 [INFO] Filled 0
2017-11-14 09:41:34,845 [INFO] NFilled 0
2017-11-14 09:41:34,845 [INFO] Single-End Reduced 0
2017-11-14 09:41:34,845 [INFO] Double-End Reduced 0

Hmmm, no gaps filled or anything, but this did produce a FASTA file. Let's just check that it actually has someting in it.

In [15]:

ls -lh /home/sam/analyses/20171114_oly_pbjelly/jelly.out.fasta

-rw-rw-r-- 1 sam sam 752M Nov 14 09:59 /home/sam/analyses/20171114_oly_pbjelly/jelly.out.fasta

Copied to owl. Had to do so outside of notebook in order to use `sudo` for copying.¶

In [16]:

ls /mnt/owl/Athaliana/20171114_oly_pbjelly/

assembly/            jelly.out.qual      output.err    support/
gap_fill_status.txt  liftOverTable.json  output.out
jelly.out.fasta      mapping/            Protocol.xml

In [ ]:

Need reference assembly of Illumina data.¶

View the Protocol.xml file tha PB Jelly uses to run.¶

Source (i.e. load) the PB Jelly setup script and run PB Jelly.¶

PB Jelly has 5 steps that must be run sequentially:¶

Copied to owl. Had to do so outside of notebook in order to use sudo for copying.¶

Copied to owl. Had to do so outside of notebook in order to use `sudo` for copying.¶