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fangly / hitman

HIgh Throughput Microbial ANalysis
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"java.io.NotSerializableException" error #1

Open kyclark opened 8 years ago

kyclark commented 8 years ago

When running "hitman_deploy," I am getting the error below. Any suggestions?

Ken

[hpc:service0@/rsgrps/bhurwitz/hurwitzlab/tools/hitman/scripts]$ ./hitman_deploy --dir /rsgrps/bhurwitz/hurwitzlab/amplicon-illumina/03_hitman_deploy_out_kyc --input /rsgrps/bhurwitz/hurwitzlab/amplicon-illumina/02_hitman_hire_out_kyc/MockRun3hdrV4.R1.merge_pairs.assembled.MockRun3hdrV4.rename_seqs.cat_files.fastq -p SKIP_DENOISING=1 -p TRIM_LEN=250
====================================================================================================
|                              Starting Pipeline at 2016-06-08 14:34                               |
====================================================================================================

========================================= Stage seq_stats ==========================================
Exception in thread "Thread-8" java.io.NotSerializableException: bpipe.PipelineOutput
    at java.io.ObjectOutputStream.writeObject0(Unknown Source)
    at java.io.ObjectOutputStream.writeObject(Unknown Source)
fangly commented 8 years ago

Hello Ken, Does the fastq output file produced by the previous hitman_hire step look good? Were there any warnings in the hire or deploy steps? Did you previously run the complete hitman workflow successfully or is it your first time? If it is, it may be bad software versions. Bpipe used to not work with the latest java version, for example. Best, Florent

On 8 Jun 2016 11:38 pm, "Ken Youens-Clark" notifications@github.com wrote:

When running "hitman_deploy," I am getting the error below. Any suggestions?

Ken

[hpc:service0@/rsgrps/bhurwitz/hurwitzlab/tools/hitman/scripts]$ ./hitman_deploy --dir /rsgrps/bhurwitz/hurwitzlab/amplicon-illumina/03_hitman_deploy_out_kyc --input /rsgrps/bhurwitz/hurwitzlab/amplicon-illumina/02_hitman_hire_out_kyc/MockRun3hdrV4.R1.merge_pairs.assembled.MockRun3hdrV4.rename_seqs.cat_files.fastq -p SKIP_DENOISING=1 -p TRIM_LEN=250 | Starting Pipeline at 2016-06-08 14:34 |

========================================= Stage seq_stats

Exception in thread "Thread-8" java.io.NotSerializableException: bpipe.PipelineOutput at java.io.ObjectOutputStream.writeObject0(Unknown Source) at java.io.ObjectOutputStream.writeObject(Unknown Source)

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