Viewing BLAST Results

Viewing BLAST results saved to a persistent volume

The run of the stock BLAST workflow template saves results to a persistent volume. You can access and post-process these results from other Fuzzball workflows by mounting the same persistent volume in other Fuzzball workflows like, for example, Jupyter or an interactive shell. In the following example we will use the Fuzzball CLI to start a workflow that will sleep until it times out or we stop it and then connect to it to access the blast results

$ fuzzball run --image docker://rockylinux:9 --volume user/persistent:/data --tty -- /bin/bash
Workflow "4489d93f-b2a8-4255-bc68-b41842dbe4c5" started.
Waiting for job to start...

(fuzzball:/)$ cd /data/results/blast

(fuzzball:/data/results/blast)$ ls -lh
total 20K
drwxrwxr-x. 2 root 100114 6.0K Apr  3 14:32 0599b2c7-1880-45cc-bbf6-b6dbfc48e8fb
drwxrwxr-x. 2 root 100114 6.0K Feb 17 16:52 10e37052-831b-496a-93de-4192b25fb138
drwxrwxr-x. 2 root 100114 6.0K Oct 10 14:33 74932c0c-d164-4c62-994d-90fd84f64052
drwxrwxr-x. 2 root 100114 6.0K Oct 10 15:39 98e0ce1a-686b-40a5-8b59-ddba76830817
drwxrwxr-x. 2 root 100114 6.0K Feb 17 03:51 b41cec31-9fb7-4e82-9153-fab52c57dc47

(fuzzball:/data/results/blast)$ head -35 b41cec31-9fb7-4e82-9153-fab52c57dc47/pox_efc.blast.out
BLASTP 2.16.0+


Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.


Reference for composition-based statistics: Alejandro A. Schaffer,
L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri
I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
"Improving the accuracy of PSI-BLAST protein database searches with
composition-based statistics and other refinements", Nucleic Acids
Res. 29:2994-3005.



Database: PDB protein database
           175,659 sequences; 50,420,065 total letters



Query= YP_232915.1 serine protease inhibitor-like [Orthopoxvirus vaccinia]

Length=369
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

4KDS_A Chain A, Plasminogen activator inhibitor 1 [Oncorhynchus m...  153     3e-42
1DB2_A Chain A, PLASMINOGEN ACTIVATOR INHIBITOR-1 [Homo sapiens]      149     7e-41
3EOX_A Chain A, Plasminogen activator inhibitor 1 [Homo sapiens]      149     8e-41
1DVN_A Chain A, PLASMINOGEN ACTIVATOR INHIBITOR-1 [Homo sapiens]      148     2e-40
4AQH_A Chain A, PLASMINOGEN ACTIVATOR INHIBITOR 1 [Homo sapiens]      148     2e-40
1C5G_A Chain A, PLASMINOGEN ACTIVATOR INHIBITOR-1 [Homo sapiens]      148     2e-40

(fuzzball:/data/results/blast)$ exit

Viewing BLAST results saved to S3

In a previous section, we created a modified workflow template that saved its BLAST result file {{.RunName}}.blast.out to an S3 bucket at destination s3://<bucket>/<path...>. In our example the saved object was s3://co-ciq-misc-support/results/pox_efc.blast.out which is what we will use below.

One method to download the results file to your workstation and view it is to use the AWS CLI to interface with the S3 bucket where your results are stored. If you do not have the AWS CLI installed, please see the AWS CLI installation instructions for more information.

Using the AWS CLI command aws s3 cp, the result file can be downloaded to your workstation. The command below copies the result file at S3 URI s3://<bucket>/<path...>/{{.RunName}}.blast.out to your working directory.

$ aws s3 cp s3://co-ciq-misc-support/results/pox_efc.blast.out .

From there you can use any standard tools to view, parse or process the BLAST output format you choose.

$ cat pox_efc.blast.out
BLASTP 2.16.0+


Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.


Reference for composition-based statistics: Alejandro A. Schaffer,
L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri
I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
"Improving the accuracy of PSI-BLAST protein database searches with
composition-based statistics and other refinements", Nucleic Acids
Res. 29:2994-3005.



Database: PDB protein database
           170,598 sequences; 48,617,182 total letters



Query= YP_233018.1 A16

Length=377
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

8GP6_A Chain A, Virion membrane protein A16 [Vaccinia virus WR]       720     0.0
7AE2_B Chain B, MNT ANTITOXIN [Aphanizomenon flos-aquae 2012/KM1/D3]  30.8    2.7
3G02_A Chain A, Epoxide hydrolase [Aspergillus niger]                 30.0    8.6
1QO7_A Chain A, EPOXIDE HYDROLASE [Aspergillus niger]                 30.0    9.0


>8GP6_A Chain A, Virion membrane protein A16 [Vaccinia virus WR]
Length=348

 Score = 720 bits (1859),  Expect = 0.0, Method: Compositional matrix adjust.
 Identities = 342/342 (100%), Positives = 342/342 (100%), Gaps = 0/342 (0%)

Query  1    MGAAVTLNRIKIAPGIADIRDKYMELGFNYPEYNRAVKFAEESYTYYYETSPGEIKPKFC  60
            MGAAVTLNRIKIAPGIADIRDKYMELGFNYPEYNRAVKFAEESYTYYYETSPGEIKPKFC
Sbjct  1    MGAAVTLNRIKIAPGIADIRDKYMELGFNYPEYNRAVKFAEESYTYYYETSPGEIKPKFC  60
...snip...