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leepc12 avatar leepc12 commented on June 27, 2024

We already figured this out. This error will be fixed soon by end of this week.

from atac-seq-pipeline.

leepc12 avatar leepc12 commented on June 27, 2024

Fixed. please update (git pull) the pipeline and try again.

If you are using a Conda environment. Update pipeline source files in the Conda env by running the following command.

$ bash conda/update_conda_env.sh

from atac-seq-pipeline.

hoholee avatar hoholee commented on June 27, 2024

Sorry to re-open this issue, but I got a similar error when using hg19 genome downloaded using the download_geome_data.sh script. And the REG2MAP_BED filed is still missing in the script:

if [[ "${GENOME}" == "hg19" ]]; then
REGEX_BFILT_PEAK_CHR_NAME="chr[\dXY]+"
MITO_CHR_NAME="chrM"
REF_FA="http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/referenceSequences/male.hg19.fa.gz"
REF_MITO_FA="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/male.hg19.chrM.fa.gz"
CHRSZ="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/hg19.chrom.sizes"
BWT2_IDX="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/bowtie2_index/male.hg19.fa.tar"
BWT2_MITO_IDX="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/bowtie2_index/male.hg19.chrM.fa.tar"
BWA_IDX="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/bwa_index/male.hg19.fa.tar"
BWA_MITO_IDX="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/bwa_index/male.hg19.chrM.fa.tar"
BLACKLIST="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/wgEncodeDacMapabilityConsensusExcludable.bed.gz"
TSS="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/ataqc/hg19_gencode_tss_unique.bed.gz"
DNASE="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz"
PROM="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/ataqc/reg2map_honeybadger2_dnase_prom_p2.bed.gz"
ENH="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/ataqc/reg2map_honeybadger2_dnase_enh_p2.bed.gz"
REG2MAP="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/ataqc/dnase_avgs_reg2map_p10_merged_named.pvals.gz"
ROADMAP_META="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/ataqc/eid_to_mnemonic.txt"

from atac-seq-pipeline.

leepc12 avatar leepc12 commented on June 27, 2024

Fixed in commit a3512e4.
This will be fixed in the next release.

from atac-seq-pipeline.

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