Notebook

Running in Docker container on Swoose¶

Started Docker container with the following command:

docker run -p 8888:8888 -v /home/sam/data/pacbio_oly/:/home/data -v /mnt/owl/:/home/owl -it bioinformatics/bioinformatics:v0 /bin/bash

The command allows /home/sam/data/ and mnt/owl (our server Owl) to be accessible to the Docker container.

Once access to Jupyter Notebook over port 8888 and makes my Jupyter Notebook GitHub repo and my data files the container was started, started Jupyter Notebook with the following command inside the Docker container:

jupyter notebook --allow-root

This is configured in the Docker container to launch a Jupyter Notebook without a browser on port 8888. The Docker container is running on an image created from this Dockerfile (Git commit 63d36ab)

In [2]:

%%bash
echo "TODAY'S DATE"
date
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh

TODAY'S DATE
Mon Oct 23 20:06:31 UTC 2017

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

Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                24
On-line CPU(s) list:   0-23
Thread(s) per core:    2
Core(s) per socket:    6
Socket(s):             2
NUMA node(s):          1
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 44
Model name:            Intel(R) Xeon(R) CPU           X5670  @ 2.93GHz
Stepping:              2
CPU MHz:               2925.850
BogoMIPS:              5851.96
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              12288K
NUMA node0 CPU(s):     0-23

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

Memory Specs

             total       used       free     shared    buffers     cached
Mem:           70G        70G       588M       244M       387M        61G
-/+ buffers/cache:       8.2G        62G
Swap:         4.7G       1.1G       3.6G

In [3]:

%%bash
hostname

1d27ba8eb17b

In [4]:

%%bash
pwd

/home/data

Print list of Illumina files for easy copying/pasting into redundans command¶

In [5]:

%%bash
for i in 1[56]*
do
echo "$i"
done

151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz

Print list of PacBio files for easy copying/pasting into redundans command¶

In [6]:

%%bash
cd ..
for i in m*
do
echo "$i"
done

m*

In [7]:

cd /home/data

/home/data

In [8]:

%%bash
for i in m*
do
echo "$i"
done

m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq.gz
m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz
m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz
m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz
m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz
m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz
m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz
m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz
m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz
m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz
m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz

In [9]:

%%bash
mkdir 20171023_oly_redundans_01

In [1]:

cd /home/data/

/home/data

This notebook crashed while running yesterday. Updated the Dockerfile used to create this container and restarted today.

In [2]:

%%bash
echo "TODAY'S DATE"
date
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh

TODAY'S DATE
Tue Oct 24 15:10:23 UTC 2017

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

Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                24
On-line CPU(s) list:   0-23
Thread(s) per core:    2
Core(s) per socket:    6
Socket(s):             2
NUMA node(s):          1
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 44
Model name:            Intel(R) Xeon(R) CPU           X5670  @ 2.93GHz
Stepping:              2
CPU MHz:               2925.850
BogoMIPS:              5851.96
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              12288K
NUMA node0 CPU(s):     0-23

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

Memory Specs

             total       used       free     shared    buffers     cached
Mem:           70G        48G        22G       265M       1.0G        38G
-/+ buffers/cache:       8.3G        62G
Swap:         4.7G       1.0G       3.6G

In [3]:

%%bash
hostname

5db143d2402e

In [4]:

ls

151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz
20171023_docker_oly_redundans.ipynb
20171023_docker_oly_redundans_01/
m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq.gz
m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz*
m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz*
m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz*
m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz*
m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz*
m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz*
m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz*
m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz*
m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz*
m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz*

In [5]:

ls

151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz
20171018_oly_pacbio.contigs.fasta
20171023_docker_oly_redundans.ipynb
20171023_docker_oly_redundans_01/
m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq.gz
m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz*
m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz*
m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz*
m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz*
m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz*
m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz*
m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz*
m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz*
m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz*
m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz*

In [6]:

!python /usr/local/bioinformatics/redundans/redundans.py \
-t 24 \
-l \
m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq.gz \
m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz \
m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz \
m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz \
m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz \
m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz \
m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz \
m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz \
m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz \
m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz \
m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz \
-i \
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz \
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz \
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz \
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz \
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz \
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz \
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz \
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz \
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz \
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz \
-f \
20171018_oly_pacbio.contigs.fasta \
-o \
/home/data/20171023_docker_oly_redundans_01/

Traceback (most recent call last):
  File "/usr/local/bioinformatics/redundans/redundans.py", line 22, in <module>
    import commands, os, resource, sys
ModuleNotFoundError: No module named 'commands'

In [7]:

!python /usr/local/bioinformatics/redundans/redundans.py \
-t 24 \
-l \
m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq.gz \
m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz \
m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz \
m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz \
m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz \
m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz \
m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz \
m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz \
m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz \
m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz \
m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz \
-i \
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz \
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz \
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz \
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz \
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz \
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz \
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz \
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz \
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz \
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz \
-f \
20171018_oly_pacbio.contigs.fasta \
-o \
/home/data/20171023_docker_oly_redundans_01/

Traceback (most recent call last):
  File "/usr/local/bioinformatics/redundans/redundans.py", line 22, in <module>
    import commands, os, resource, sys
ModuleNotFoundError: No module named 'commands'

Some searching reveals that "commands" is no longer available in Python3; need to use Python2...

Running in Docker container on Swoose¶

Started Docker container with the following command:

docker run -p 8888:8888 -v /home/sam/data/pacbio_oly/:/home/data -v /mnt/owl/:/home/owl -it bioinformatics/bioinformatics:v0 /bin/bash

The command allows /home/sam/data/ to be accessible to the Docker container.

jupyter notebook --allow-root

This is configured in the Docker container to launch a Jupyter Notebook without a browser on port 8888. The Docker container is running on an image created from this Dockerfile (Git commit e38d24bd)

In [1]:

%%bash
echo "TODAY'S DATE"
date
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh

TODAY'S DATE
Tue Oct 24 17:16:40 UTC 2017

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

Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                24
On-line CPU(s) list:   0-23
Thread(s) per core:    2
Core(s) per socket:    6
Socket(s):             2
NUMA node(s):          1
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 44
Model name:            Intel(R) Xeon(R) CPU           X5670  @ 2.93GHz
Stepping:              2
CPU MHz:               2925.850
BogoMIPS:              5851.96
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              12288K
NUMA node0 CPU(s):     0-23

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

Memory Specs

             total       used       free     shared    buffers     cached
Mem:           70G        61G       9.5G       454M       1.2G        51G
-/+ buffers/cache:       8.8G        61G
Swap:         4.7G       1.0G       3.6G

In [2]:

%%bash
hostname

8358b3f2ee6e

In [3]:

ls

151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz
20171018_oly_pacbio.contigs.fasta
20171023_docker_oly_redundans.ipynb
20171023_docker_oly_redundans_01/
m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq.gz
m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz*
m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz*
m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz*
m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz*
m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz*
m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz*
m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz*
m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz*
m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz*
m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz*

In [4]:

!python /usr/local/bioinformatics/redundans/redundans.py \
-t 24 \
-l \
m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq.gz \
m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz \
m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz \
m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz \
m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz \
m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz \
m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz \
m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz \
m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz \
m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz \
m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz \
-i \
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz \
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz \
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz \
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz \
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz \
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz \
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz \
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz \
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz \
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz \
-f \
20171018_oly_pacbio.contigs.fasta \
-o \
/home/data/20171023_docker_oly_redundans_01/

Directory /home/data/20171023_docker_oly_redundans_01/ exists!

In [5]:

%%bash
rmdir 20171023_docker_oly_redundans_01/

In [ ]:

!python /usr/local/bioinformatics/redundans/redundans.py \
-t 24 \
-l \
m130619_081336_42134_c100525122550000001823081109281326_s1_p0.fastq.gz \
m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz \
m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz \
m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz \
m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz \
m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz \
m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz \
m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz \
m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz \
m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz \
m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz \
-i \
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz \
151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz \
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz \
151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz \
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz \
151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz \
160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz \
160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz \
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz \
160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz \
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz \
160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz \
-f \
20171018_oly_pacbio.contigs.fasta \
-o \
/home/data/20171023_docker_oly_redundans_01/

In [ ]: