cp --remove-destination does not work on OS

[elhamazizi]

Error when running install_genome_data.sh on OS:

Extracting/processing data files... cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory

[leepc12]

Please follow the instruction I sent you via email and let us know if it works. Then we will make a hotfix for Mac OS.

[siyunw]

I also have a error when running bash install_genome_data.sh hg19 datadir

AttributeError: module 'enum' has no attribute 'IntFlag'

Do you know how i could avoid this error?

[leepc12]

@siyunw Can you post a full error log here? Which OS did you use?

[siyunw]

this time the error is "tar: Child returned status 1 tar: Error is not recoverable: exiting now"

Here is the full log: This script installs data for genome [GENOME] on a directory [DATA_DIR]. Genome data files will be installed on [DATA_DIR]/[GENOME]. A species file [DATA_DIR]/bds_atac_species.conf will be generated and added to default.conf.

Supported genomes: hg19, mm9, hg38 and mm10

Usage: ./install_genome_data.sh [GENOME] [DATA_DIR] Example: ./install_genome_data.sh hg19 /genome_data

[slwang]:$ bash install_genome_data.sh hg19 data_dir_hg19

Downloading files... --2017-11-02 16:15:56-- http://mitra.stanford.edu/kundaje/genome_data/hg19/globalmap_k20tok54.tgz Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 249559554 (238M) [application/x-gzip] Saving to: “globalmap_k20tok54.tgz”

100%[======================================================================================>] 249,559,554 49.6M/s in 5.0s

2017-11-02 16:16:03 (47.9 MB/s) - “globalmap_k20tok54.tgz” saved [249559554/249559554]

--2017-11-02 16:16:03-- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/referenceSequences/male.hg19.fa.gz Resolving hgdownload.cse.ucsc.edu... 128.114.119.163 Connecting to hgdownload.cse.ucsc.edu|128.114.119.163|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 936272240 (893M) [application/x-gzip] Saving to: “male.hg19.fa.gz”

100%[======================================================================================>] 936,272,240 37.6M/s in 22s

2017-11-02 16:16:26 (40.7 MB/s) - “male.hg19.fa.gz” saved [936272240/936272240]

--2017-11-02 16:16:36-- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz Resolving hgdownload.cse.ucsc.edu... 128.114.119.163 Connecting to hgdownload.cse.ucsc.edu|128.114.119.163|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 4731 (4.6K) [application/x-gzip] Saving to: “wgEncodeDacMapabilityConsensusExcludable.bed.gz”

100%[======================================================================================>] 4,731 --.-K/s in 0s

2017-11-02 16:16:37 (221 MB/s) - “wgEncodeDacMapabilityConsensusExcludable.bed.gz” saved [4731/4731]

--2017-11-02 16:16:37-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/hg19_gencode_tss_unique.bed.gz Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 235292 (230K) [application/x-gzip] Saving to: “hg19_gencode_tss_unique.bed.gz”

100%[======================================================================================>] 235,292 --.-K/s in 0.1s

2017-11-02 16:16:37 (2.27 MB/s) - “hg19_gencode_tss_unique.bed.gz” saved [235292/235292]

--2017-11-02 16:16:37-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 11219795 (11M) [application/x-gzip] Saving to: “reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz”

100%[======================================================================================>] 11,219,795 23.4M/s in 0.5s

2017-11-02 16:16:38 (23.4 MB/s) - “reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz” saved [11219795/11219795]

--2017-11-02 16:16:38-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/reg2map_honeybadger2_dnase_prom_p2.bed.gz Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 666590 (651K) [application/x-gzip] Saving to: “reg2map_honeybadger2_dnase_prom_p2.bed.gz”

100%[======================================================================================>] 666,590 3.67M/s in 0.2s

2017-11-02 16:16:38 (3.67 MB/s) - “reg2map_honeybadger2_dnase_prom_p2.bed.gz” saved [666590/666590]

--2017-11-02 16:16:38-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/reg2map_honeybadger2_dnase_enh_p2.bed.gz Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 18386700 (18M) [application/x-gzip] Saving to: “reg2map_honeybadger2_dnase_enh_p2.bed.gz”

100%[======================================================================================>] 18,386,700 25.9M/s in 0.7s

2017-11-02 16:16:39 (25.9 MB/s) - “reg2map_honeybadger2_dnase_enh_p2.bed.gz” saved [18386700/18386700]

--2017-11-02 16:16:39-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/dnase_avgs_reg2map_p10_merged_named.pvals.gz Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 154254597 (147M) [application/x-gzip] Saving to: “dnase_avgs_reg2map_p10_merged_named.pvals.gz”

100%[======================================================================================>] 154,254,597 50.4M/s in 2.9s

2017-11-02 16:16:43 (50.4 MB/s) - “dnase_avgs_reg2map_p10_merged_named.pvals.gz” saved [154254597/154254597]

--2017-11-02 16:16:43-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/eid_to_mnemonic.txt Resolving mitra.stanford.edu... 171.65.76.236 Connecting to mitra.stanford.edu|171.65.76.236|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 2340 (2.3K) [text/plain] Saving to: “eid_to_mnemonic.txt”

100%[======================================================================================>] 2,340 --.-K/s in 0s

2017-11-02 16:16:43 (181 MB/s) - “eid_to_mnemonic.txt” saved [2340/2340]

gzip: stdin: unexpected end of file tar: Child returned status 1 tar: Error is not recoverable: exiting now

[leepc12]

@siyunw, I am working on a hot fix for this. tar error an cp error will be fixed. BTW How did you fix AttributeError: module 'enum' has no attribute 'IntFlag' error?

[siyunw]

The module 'enum' has no attribute 'IntFlag' error was likely due to I have conflict versions of pythons. I log out and log in after re-installed the minoconda 3, then it showed the new error.

[leepc12]

Please get the the latest pipeline and try again.