Replies: 4 comments 2 replies
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It is generally fine without the slimming result from K45, especially when you can get the result from larger kmers in downstream disentangling. To fix it, what is there under |
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These are the files created
drwxrwsr-x 9 jhallas mbuchalski 21 Jan 31 15:46 ..
-rw-rw-r-- 1 jhallas mbuchalski 2.6K Jan 31 12:00 final.lib_data
drwxrwsr-x 3 jhallas mbuchalski 9 Jan 31 12:00 .
-rw-rw-r-- 1 jhallas mbuchalski 113M Jan 31 12:00
assembly_graph_with_scaffolds.gfa
-rw-rw-r-- 1 jhallas mbuchalski 90M Jan 31 12:00 final_contigs.fasta
-rw-rw-r-- 1 jhallas mbuchalski 90M Jan 31 11:52 simplified_contigs.fasta
-rw-rw-r-- 1 jhallas mbuchalski 296M Jan 31 11:43 assembly_graph.fastg
-rw-rw-r-- 1 jhallas mbuchalski 90M Jan 31 11:42 before_rr.fasta
drwxrwsr-x 2 jhallas mbuchalski 19 Jan 31 10:56 configs
…On Mon, Jan 30, 2023 at 5:57 PM Jianjun Jin ***@***.***> wrote:
It is generally fine without the slimming result from K45, especially when
you can get the result from larger kmers in downstream disentangling.
To fix it, what is there under
/share/cdfwwildlife/hallas_dedicated/lc_deer/mtDNA/getorganelle/DB10020/extended_spades/K45/
if you use like ls -alht.
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It looks so typical. The indices should also exist because the previous runs are good. Did you get the final result from the larger kmers? |
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I believe the larger kmers finished but I never got the final assembly
animal_mt.K85.complete.graph1.1.path_sequence.fasta
…On Wed, Feb 1, 2023 at 9:43 AM Jianjun Jin ***@***.***> wrote:
It looks so normal. The indices should also exist because the previous
runs are good.
Did you get the final result from the larger kmers?
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Which step did it get stuck in? |
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The disentangling step. This is the last line in the get_org.log file. Is
there a reason why the analysis might crash? I had similar sized files
complete.
2023-01-30 06:52:41,529 - INFO: Disentangling
/share/cdfwwildlife/hallas_dedicated/lc_deer/mtDNA/getorganelle/DB10020/extended_spades/K85/assembly_graph.fastg.extend-animal_mt.fastg
as a circular genome ...
…On Wed, Feb 1, 2023 at 11:44 AM Jianjun Jin ***@***.***> wrote:
Which step did it get stuck in?
The complete result is not guaranteed for every run or data. But you
should at least get contigs/scaffolds when the disentangling step finishes.
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Hello,
I am unsure about this error. Even though the spades.log says "SPAdes pipeline finished WITH WARNINGS!" a fasta file is not generated. After look at the get_org.log file, it looks like there was an error in slimming. So then I looked into the slim.log and it says
ERROR: BLAST Database error: No alias or index file found for nucleotide database [/home/jhallas/.GetOrganelle/LabelDatabase/animal_mt] in search path [/share/cdfwwildlife/hallas_dedicated/lc_deer/scripts::]. I assembled 79 other genomes and this is the only one that encountered this error.output from get_org.log.txt
output from warnings.log
output from slim.log K45
I am using a circular mtDNA genome from the same species as the seed. My sequencing coverage is 25X. I don't know
This is my command.
get_organelle_from_reads.py -1 $FQDIR/${ID1}_R1.fastq.gz -2 $FQDIR/${ID1}_R2.fastq.gz -k 21,45,65,85 -s $SEED --target-genome-size 16500 -F animal_mt -t 32 -o $OUTDIR/$ID1Any advise would be much appreciated. If there is more information you need please let me know.
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