Uncaught error and killed

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Ligia Catallina Muñoz Arenas

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Feb 2, 2018, 8:52:13 AM2/2/18
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Hi, I'm traying that run my clean sequences and the program shows a legend that say:
Uncaught exception: Failure("Sequence 559094.2.2.73 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 559094.2.2.73 doesn't overlap any reference sequences.")
killed

I'm not sure about my results.
Can you explain me what meaning that legend?
Thanks

Guillaume Jospin

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Feb 2, 2018, 9:08:18 AM2/2/18
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Can you provide us with the command you used and a log of what was printed please?
Using the —debug flag could be helpful in this case. 

Are you reads appropriately paired?
Are you running contigs?

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Ligia Catallina Muñoz Arenas

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Feb 2, 2018, 9:46:18 AM2/2/18
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This is de command
./phylosift all --paired /media/admins/RESPALDO/Q28/pine_oakforest_west4_paired.fastq.gz /media/admins/RESPALDO/Q28/pine_oakforest_west4_2paired.fastq.gz

My reads was cleaned with trimmomatic 0.36 with Q>28, and the reads cleaned are the input for the command. I'm not running contigs.

The log is this, here don't show the log killed but in previews words if I had it, after Fatal error and continued with other Uncaught error.


Uncaught exception: Failure("Sequence 559094.2.2.73 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 559094.2.2.73 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 73947.1.5.67 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 73947.1.5.67 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 371445.1.2.97 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 371445.1.2.97 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 321368.1.29.100 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 321368.1.29.100 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 930929.2.33.101 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 930929.2.33.101 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 579631.1.10.99 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 579631.1.10.99 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 67158.2.3.77 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 67158.2.3.77 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 11907.1.35.100 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 11907.1.35.100 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 765849.1.16.99 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 765849.1.16.99 doesn't overlap any reference sequences.")



Ligia Catallina Muñoz Arenas

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Feb 2, 2018, 9:47:56 AM2/2/18
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This is de command
./phylosift all --paired /media/admins/RESPALDO/Q28/
pine_oakforest_west4_paired.fastq.gz /media/admins/RESPALDO/Q28/pine_oakforest_west4_2paired.fastq.gz

My reads was cleaned with trimmomatic 0.36 with Q>28, and the reads cleaned are the input for the command. I'm not running contigs.

The log is this, here don't show the log killed but in previews words if I had it, after Fatal error and continued with other Uncaught error.

Uncaught exception: Failure("Sequence 559094.2.2.73 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 559094.2.2.73 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 73947.1.5.67 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 73947.1.5.67 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 371445.1.2.97 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 371445.1.2.97 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 321368.1.29.100 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 321368.1.29.100 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 930929.2.33.101 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 930929.2.33.101 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 579631.1.10.99 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 579631.1.10.99 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 67158.2.3.77 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 67158.2.3.77 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 11907.1.35.100 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 11907.1.35.100 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 765849.1.16.99 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 765849.1.16.99 doesn't overlap any reference sequences.")

Guillaume Jospin

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Feb 2, 2018, 10:21:01 AM2/2/18
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That's a lot of errors... Does it mess up your results? I'm not sure... it depends on which marker it happened on and also which step of the pipeline.
Would it be possible to send me the printout for the same command using the --debug flag?

One way to get around this would be to remove the problematic sequences...
If the pipeline finished, then everything was renamed to match the original sequences names, so the messages above aren't super informative.
If the pipeline did not finish, then you should have a lookup file in the blastDir to figure out the mapping between PhyloSift's internal renaming and the original sequences.

It might also be helpful to see if I could reproduce your error if you could provide a subset of your reads, I would give it a go.



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Ligia Catallina Muñoz Arenas

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Feb 2, 2018, 5:26:18 PM2/2/18
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 In this moment my sequences are running ( with the errors that I say yet), do you recommend stop the work? Previously I ran raw data (wtihout clean) with the same errors and I obtained a Krona, but I do not the confidence of these results. I will start a new job with the --debug flag and i will inform you about the messages

Ligia Catallina Muñoz Arenas

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Feb 2, 2018, 9:24:44 PM2/2/18
to PhyloSift
This is the latest result that show me de screen:


Uncaught exception: Failure("Sequence 559094.2.2.73 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 559094.2.2.73 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 73947.1.5.67 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 73947.1.5.67 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 371445.1.2.97 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 371445.1.2.97 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 321368.1.29.100 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 321368.1.29.100 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 930929.2.33.101 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 930929.2.33.101 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 579631.1.10.99 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 579631.1.10.99 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 67158.2.3.77 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 67158.2.3.77 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 11907.1.35.100 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 11907.1.35.100 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 765849.1.16.99 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 765849.1.16.99 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 444768.2.3.65 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 444768.2.3.65 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 192295.2.3.77 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 192295.2.3.77 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 597641.1.6.83 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 597641.1.6.83 doesn't overlap any reference sequences.")
Uncaught exception: Failure("Sequence 959474.2.3.95 doesn't overlap any reference sequences.")
Fatal error: exception Failure("Sequence 959474.2.3.95 doesn't overlap any reference sequences.")
Use of uninitialized value $inf in pattern match (m//) at /home/admins/phylosift_v1.0.1/bin/../lib/Phylosift/Utilities.pm line 2124.
Use of uninitialized value $short_rna_jplace in -e at /home/admins/phylosift_v1.0.1/bin/../lib/Phylosift/pplacer.pm line 106.
Use of uninitialized value $short_rna_jplace in -e at /home/admins/phylosift_v1.0.1/bin/../lib/Phylosift/pplacer.pm line 107.
Use of uninitialized value $short_rna_jplace in -e at /home/admins/phylosift_v1.0.1/bin/../lib/Phylosift/pplacer.pm line 109.
admins@pc1[phylosift_v1.0.1] lastal: bad FASTQ data                          []
admins@pc1[phylosift_v1.0.1]                                          
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Ligia Catallina Muñoz Arenas

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Feb 2, 2018, 9:26:16 PM2/2/18
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And this is part that the results with --debug flag

Running /home/admins/phylosift_v1.0.1/bin/pplacer  -o /home/admins/phylosift_v1.0.1/PS_temp/pine_oak_west4_paired.fastq.gz/treeDir/mtDNA_ATP6_aa_aligned.updated.1.jplace --verbosity 0 -j 1 -c /home/admins/share/phylosift/markers/mtDNA_ATP6_aa_aligned.updated "/home/admins/phylosift_v1.0.1/PS_temp/pine_oak_west4_paired.fastq.gz/alignDir/mtDNA_ATP6_aa_aligned.updated.1.fasta"
Removed 0 sequences on long pendant edges
Placing on codon markers: mtDNA_ATP6_aa_aligned
Looking for codon placeable reads
codon read jplace
Found 9 codon placeable reads
9 reads in group 1 added to /home/admins/phylosift_v1.0.1/PS_temp/pine_oak_west4_paired.fastq.gz/alignDir/mtDNA_ATP6_aa_aligned.codon.updated.sub1.1.fasta
Running /home/admins/phylosift_v1.0.1/bin/pplacer  -o /home/admins/phylosift_v1.0.1/PS_temp/pine_oak_west4_paired.fastq.gz/treeDir/mtDNA_ATP6_aa_aligned.codon.updated.sub1.1.jplace --verbosity 0 -j 1 -c /home/admins/share/phylosift/markers/mtDNA_ATP6_aa_aligned.codon.updated "/home/admins/phylosift_v1.0.1/PS_temp/pine_oak_west4_paired.fastq.gz/alignDir/mtDNA_ATP6_aa_aligned.codon.updated.sub1.1.fasta"
Removed 0 sequences on long pendant edges
Naming taxa in marker mtDNA_ATP6_aa_aligned
Trying to use /home/admins/share/phylosift/markers/mtDNA_ATP6_aa_aligned.codon.updated/mtDNA_ATP6_aa_aligned.codon.updated.taxonmap
Naming taxa in name_taxa_in_jplace for mtDNA_ATP6_aa_aligned
Done reading namemap
Naming taxa in marker mtDNA_ATP6_aa_aligned
Trying to use /home/admins/share/phylosift/markers/mtDNA_ATP6_aa_aligned.updated/mtDNA_ATP6_aa_aligned.updated.taxonmap
Naming taxa in name_taxa_in_jplace for mtDNA_ATP6_aa_aligned
Done reading namemap
Running /home/admins/phylosift_v1.0.1/bin/pplacer  -o /home/admins/phylosift_v1.0.1/PS_temp/pine_oak_west4_paired.fastq.gz/treeDir/V486.updated.1.jplace --verbosity 0 -j 1 -c /home/admins/share/phylosift/markers/V486.updated "/home/admins/phylosift_v1.0.1/PS_temp/pine_oak_west4_paired.fastq.gz/alignDir/V486.updated.1.fasta"
Removed 1 sequences on long pendant edges
Placing on codon markers: V486
Looking for codon placeable reads
codon read jplace
Found 0 codon placeable reads



El viernes, 2 de febrero de 2018, 9:21:01 (UTC-6), Guillaume Jospin escribió:
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