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albacore's Introduction

albacore

Dockerfile for the Albacore basecaller from Oxford Nanopore

usage

cd into the directory containing the reads directory

docker run -v $PWD:$PWD -w $PWD -u $UID \
vera/albacore \
--recursive \
-t $(nproc) \
-i reads \
-c /opt/albacore/r94_450bps_linear.cfg \
-s output \

Available flowcell + kit combinations are:

flowcell kit barcoding config file
FLO-MIN106 SQK-LSK108 r94_450bps_linear.cfg
FLO-MIN106 SQK-LSK208 r94_250bps_2d.cfg
FLO-MIN106 SQK-LWB001 included r94_450bps_linear.cfg
FLO-MIN106 SQK-LWP001 r94_450bps_linear.cfg
FLO-MIN106 SQK-RAB201 included r94_450bps_linear.cfg
FLO-MIN106 SQK-RAD002 r94_450bps_linear.cfg
FLO-MIN106 SQK-RAS201 r94_450bps_linear.cfg
FLO-MIN106 SQK-RBK001 included r94_450bps_linear.cfg
FLO-MIN106 SQK-RLB001 included r94_450bps_linear.cfg
FLO-MIN106 SQK-RLI001 r94_450bps_linear.cfg
FLO-MIN106 SQK-RNA001 r94_70bps_rna_linear.cfg
FLO-MIN106 VSK-VBK001 r94_450bps_linear.cfg

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jgi-bioinformatics 0820ll thanhleviet lqsae

albacore's Issues

fast5 Could not extract read data from file error

Hi
does anybody got this error while running albcore from the docker: these are the first lines of the pipeline.log
2019-05-30 10:04:56,759 ONT Albacore Sequencing Pipeline Software (version 1.1.1)
2019-05-30 10:04:56,760 Debug level is 0
2019-05-30 10:04:57,429 Submitting file "FAK51411_cdead9df53686dbe5ce09de1dba69fd434c80e06_18.fast5".
2019-05-30 10:04:57,437 Could not extract read data from file "FAK51411_cdead9df53686dbe5ce09de1dba69fd434c80e06_18.fast5".
2019-05-30 10:04:57,438 Submitting file "FAK51411_cdead9df53686dbe5ce09de1dba69fd434c80e06_9.fast5".

thanks
ib

Problems with base calling in fast5 and fastq format

Hi,

I did the base calling with the option -o fastq,fast5 and --files_per_batch_folder 0
I did got all the fast5 files sorted in the workspace directory but I can't find the fastq file. Where is it supposed to end ?
Can albacore convert fast5 files to fastq ?

Thank you very much,

Empty results

I use the albacore the call the fast5 file. However the resulting workspace file was empty.

Here is the linux shell:
read_fast5_basecaller.py -i /home/yuxin/home/yuxin/Nanopore/DATA/HEK293_shMETTL3/fast5 -r -t 5 -f FLO-MIN107 --k SQK-RNA001 -s /home/yuxin/home/yuxin/Nanopore/DATA/HEK293_shMETTL3/fastq
| 278 of 278|################################################|100% Time: 0:00:00

new version of albacore

Dear Daniel,

do you plan to put the latest version of albacore (v1.0) in the docker container?
Would be great!
thanks a lot
cheers

Mathilde

read_fast5_basecaller.py", line 477, in <module> config_override = parse_config_override(unknown_args) 

docker run docker.io/robegan21/albacore read_fast5_basecaller.py read_fast5_basecaller.py -f FLO-PRO002 -k SQK-LSK109 -t 8 -i E:/Documents/Rwork/Data/Nanopore/results/00_ref_and_rawdata/PAQ84345_pass_barcode11_d1ae855a_f9dd6d43_0.fast5 -s E:/Documents/Rwork/Data/Nanopore/results/00_ref_and_rawdata/ -o fastq
Traceback (most recent call last):
  File "/usr/bin/read_fast5_basecaller.py", line 477, in <module>
    config_override = parse_config_override(unknown_args)
  File "/usr/lib/python3/dist-packages/albacore/config_utils.py", line 107, in parse_config_override
    raise Exception('Unknown command-line argument ' + option)
Exception: Unknown command-line argument read_fast5_basecaller.py

I'm running albacore on docker desktop,and meet such a problem.

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