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Georgehe4 / NPM command line
Last active October 19, 2018 00:10
Error Debugging - NPM
npm start
> @ start /Users/george/cs242/f18-assignments/assign4/program
> webpack-dev-server -d --open
ℹ ｢wds｣: Project is running at http://localhost:8080/
ℹ ｢wds｣: webpack output is served from /
ℹ ｢wdm｣: Hash: 4cf8f265c24962ca9c0b
Version: webpack 4.20.2
Time: 3366ms
@Georgehe4
Georgehe4 / make command (top level)
Last active September 5, 2018 01:27
NPM error - Mango Viz
sudo make develop
python2.7: can't open file 'version.py': [Errno 2] No such file or directory
pip install -e .
Obtaining file:///home/george/mango/mango-viz
Complete output from command python setup.py egg_info:
setup.py entered
$PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
running egg_info
running jsdeps
1.4.21
@Georgehe4
Georgehe4 / issue.txt
Created April 13, 2018 03:46
Python startup issue in docker
GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
sc
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/opt/cgl-docker-lib/mango/mango-assembly/target/mango-assembly-0.0.1-SNAPSHOT.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/usr/lib/hadoop/lib/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
Downloading gs://mango-initialization-bucket/google-cloud-nio-0.22.0-alpha-shaded.jar to /tmp/tmp4465580292933670773/google-cloud-nio-0.22.0-alpha-shaded.jar.
Setting default log level to "WARN".
@Georgehe4
Georgehe4 / main.dart
Created March 15, 2018 21:27
Test Gist
test
@Georgehe4
Georgehe4 / output.txt
Created February 28, 2018 05:13
Successful Adam-Submit
adam$ bin/adam-submit --jars=gs://mango-initialization-bucket/google-cloud-nio-0.22.0-alpha-shaded.jar -- transformAlignments gs://mango-initialization-bucket/HG01384.mapped.ILLUMINA.bwa.CLM.low_coverage.20120522.bam gs://mango-initialization-bucket/HG01384.mapped.ILLUMINA.bwa.CLM.low_coverage.20120522_transformed_new.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/usr/bin/spark-submit
xxxxxx---- USING ADAM CLI JAR /home/george/adam/adam-assembly/target/adam-assembly-spark2_2.11-0.24.0-SNAPSHOT.jar
18/02/28 04:37:37 INFO com.google.cloud.hadoop.fs.gcs.GoogleHadoopFileSystemBase: GHFS version: 1.6.3-hadoop2
Downloading gs://mango-initialization-bucket/google-cloud-nio-0.22.0-alpha-shaded.jar to /tmp/tmp3395184979763179247/google-cloud-nio-0.22.0-alpha-shaded.jar.
18/02/28 04:37:38 INFO org.bdgenomics.adam.cli.ADAMMain: ADAM invoked with args: "transformAlignments" "gs://mango-initialization-bucket/HG01384.mapped.ILLUMINA.bwa.CLM.low_coverage.20120522.bam" "gs://mango-initialization-bu
@Georgehe4
Georgehe4 / failure.txt
Last active February 28, 2018 04:31
Failed ADAM command using --packages. google cloud nio
18/02/28 04:26:52 INFO org.apache.hadoop.yarn.client.api.impl.YarnClientImpl: Submitted application application_1519790048472_0003
18/02/28 04:27:13 INFO org.bdgenomics.adam.rdd.ADAMContext: Loading gs://mango-initialization-bucket/HG01384.mapped.ILLUMINA.bwa.CLM.low_coverage.20120522.bam as BAM/CRAM/SAM and converting to AlignmentRecords.
18/02/28 04:27:14 INFO org.bdgenomics.adam.rdd.ADAMContext: Loaded header from gs://mango-initialization-bucket/HG01384.mapped.ILLUMINA.bwa.CLM.low_coverage.20120522.bam
18/02/28 04:27:17 INFO org.bdgenomics.adam.serialization.ADAMKryoRegistrator: Did not find Spark internal class. This is expected for earlier Spark versions.
18/02/28 04:27:18 INFO org.bdgenomics.adam.rdd.read.RDDBoundAlignmentRecordRDD: Saving data in ADAM format
18/02/28 04:27:19 INFO org.apache.hadoop.mapreduce.lib.input.FileInputFormat: Total input files to process : 1
18/02/28 04:27:33 INFO org.bdgenomics.adam.serialization.ADAMKryoRegistrator: Did not find Spark internal class. This is expected for ea
@Georgehe4
Georgehe4 / Error.txt
Created January 20, 2018 06:10
Mango errors
Py4JJavaError: An error occurred while calling o66.collectToPython.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 4 times, most recent failure: Lost task 0.3 in stage 0.0 (TID 3, mango-2-w-0.c.mango-bdgenomics.internal, executor 1): java.lang.IllegalStateException: unread block data
at java.io.ObjectInputStream$BlockDataInputStream.setBlockDataMode(ObjectInputStream.java:2740)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1567)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2245)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2169)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2027)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1535)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:422)
at org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:75)
@Georgehe4
Georgehe4 / docker-install.sh
Last active November 25, 2017 06:06
docker Instance on debian
#/bin/bash
# install packages to allow apt to use a repository over HTTPS:
sudo apt-get -y install \
apt-transport-https ca-certificates curl software-properties-common
# add Docker’s official GPG key:
curl -fsSL https://download.docker.com/linux/debian/gpg | sudo apt-key add -
# set up the Docker stable repository.
sudo add-apt-repository \
"deb [arch=amd64] https://download.docker.com/linux/debian \
$(lsb_release -cs) \
@Georgehe4
Georgehe4 / README.md
Last active August 29, 2015 14:26
@Georgehe4
Georgehe4 / TestWorld
Created May 12, 2015 22:42
print("Hello world")