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BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data
http://pellegrini.mcdb.ucla.edu/BS_Seeker2/
MIT License
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ERROR: Index DIR "_rrbs_150_400.." cannot be found in /home/knight05/software/BSseeker2-2.1.1/bs_utils/reference_genomes. Please run the bs_seeker2-build.py to create it with the correct parameters for -g, -r, --low, --up and --aligner. #28

Closed connorhknight closed 5 years ago

connorhknight commented 5 years ago

Hi, I am receiving the error above when trying to use the aligner. I have run the bs_seeker2-build.py script on my reference genome. I have also been specifying the up and low bound too. Any advice?

guoweilong commented 5 years ago

Could you paste your full commands for building the index and alignment step?

connorhknight commented 5 years ago

python bs_seeker2-build.py -file /home/knight05/data/BSeeker_ref/ --aligner=bowtie2 -p -r -l 150 _u 400

python bs_seeker2-align.py -1 /store/LevelOne/ATAC_FFPE/METHYLATION/RRBS/UCL_pilot_01/diversity_trimmed/TR0008_S6_R1_001_val_1.fq_trimmed.fq.gz -2 /store/LevelOne/ATAC_FFPE/METHYLATION/RRBS/UCL_pilot_01/diversity_trimmed/TR0008_S6_R3_001_val_2.fq_trimmed.fq.gz -g -r

From: Weilong Guo notifications@github.com Sent: 12 July 2019 08:15 To: BSSeeker/BSseeker2 Cc: Connor Knight; Author Subject: Re: [BSSeeker/BSseeker2] ERROR: Index DIR "_rrbs_150_400.." cannot be found in /home/knight05/software/BSseeker2-2.1.1/bs_utils/reference_genomes. Please run the bs_seeker2-build.py to create it with the correct parameters for -g, -r, --low, --...

Could you paste your full commands for building the index and alignment step?

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guoweilong commented 5 years ago

As you have built specific RRBS index, you need to use same "-r -L -U" parameters for alignment step.

python bs_seeker2-align.py -1 /store/LevelOne/ATAC_FFPE/METHYLATION/RRBS/UCL_pilot_01/diversity_trimmed/TR0008_S6_R1_001_val_1.fq_trimmed.fq.gz -2 /store/LevelOne/ATAC_FFPE/METHYLATION/RRBS/UCL_pilot_01/diversity_trimmed/TR0008_S6_R3_001_val_2.fq_trimmed.fq.gz -g -r -L 150 -U 400.

Best,

Weilong

At 2019-07-12 20:34:03, "Connor Knight" notifications@github.com wrote: python bs_seeker2-build.py -file /home/knight05/data/BSeeker_ref/ --aligner=bowtie2 -p -r -l 150 _u 400

python bs_seeker2-align.py -1 /store/LevelOne/ATAC_FFPE/METHYLATION/RRBS/UCL_pilot_01/diversity_trimmed/TR0008_S6_R1_001_val_1.fq_trimmed.fq.gz -2 /store/LevelOne/ATAC_FFPE/METHYLATION/RRBS/UCL_pilot_01/diversity_trimmed/TR0008_S6_R3_001_val_2.fq_trimmed.fq.gz -g -r

From: Weilong Guo notifications@github.com Sent: 12 July 2019 08:15 To: BSSeeker/BSseeker2 Cc: Connor Knight; Author Subject: Re: [BSSeeker/BSseeker2] ERROR: Index DIR "_rrbs_150_400.." cannot be found in /home/knight05/software/BSseeker2-2.1.1/bs_utils/reference_genomes. Please run the bs_seeker2-build.py to create it with the correct parameters for -g, -r, --low, --...

Could you paste your full commands for building the index and alignment step?

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