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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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error in install HiC-Pro-2.11.1 #318

Closed shiyi-pan closed 4 years ago

shiyi-pan commented 4 years ago

My python version is 3.6.5. when i installed the HiC-Pro-2.11.1, I faced an error like that : NameError: name 'cmp' is not defined. I searched the internet and found all python version is 3.X don't has the 'cmp' function,so how can I fix the error?

AnthonyJaquaniello commented 4 years ago

Hello, Sorry but HiC-Pro is designed only for python 2.X distributions, please retry with python version > 2.7

shiyi-pan commented 4 years ago

hi, Thank you for your reply. I changed my python version and installed HiC-Pro .when I ran the secprit, I mat an error like that :

Bowtie2 alignment step1 ... Logs: logs/dixon_2M_2/mapping_step1.log /ds3512/home/panyp/ruanjian/HiC-Pro/HiC-Pro_2.11.1/scripts/hic.inc.sh: line 86: bowtie_results/bwt2_global/dixon_2M_2/SRR400264_01R2/ds3512/home/panyp/Hi-C /annotation/hg19.bwt2glob.bam: No such file or directory /ds3512/home/panyp/ruanjian/HiC-Pro/HiC-Pro_2.11.1/scripts/hic.inc.sh: line 86: bowtie_results/bwt2_global/dixon_2M_2/SRR400264_01R1/ds3512/home/panyp/Hi-C /annotation/hg19.bwt2glob.bam: No such file or directory Exit: Error in reads alignment - Exit make: *** [bowtie_global] Error 1

Is my configure file wrong? I changed as that:

Alignment options

####################################################################### MIN_MAPQ = 0 BOWTIE2_IDX_PATH = /ds3512/home/panyp/Hi-C/annotation/ BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder BOWTIE2_LOCAL_OPTIONS =  --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder #######################################################################

Annotation files

####################################################################### REFERENCE_GENOME = /ds3512/home/panyp/Hi-C/annotation/hg19 GENOME_SIZE = /ds3512/home/panyp/Hi-C/annotation/chrom_hg19.sizes

Digestion Hi-C

####################################################################### GENOME_FRAGMENT = /ds3512/home/panyp/Hi-C/annotation/HindIII_resfrag_hg19.bed .

------------------ 原始邮件 ------------------ 发件人: "AnthonyJaquaniello"<notifications@github.com>; 发送时间: 2020年3月3日(星期二) 晚上9:26 收件人: "nservant/HiC-Pro"<HiC-Pro@noreply.github.com>; 抄送: "梦"<1343213784@qq.com>;"Author"<author@noreply.github.com>; 主题: Re: [nservant/HiC-Pro] error in install HiC-Pro-2.11.1 (#318)

Hello, Sorry but HiC-Pro is designed only for python 2.X distributions, please retry with python version > 2.7

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shiyi-pan commented 4 years ago

I fixed it by remove the full path in REFERENCE_GENOME and GENOME_SIZE

AnthonyJaquaniello commented 4 years ago

Hello,

According to the documentation, REFERENCE_GENOME is just the genome prefix used for genome indexes, as hg19 for example. About GENOME_SIZE, the file is loaded from the ANNOTATION folder in the HiC-Pro installation directory, you just need to put the file name.

Le mer. 4 mars 2020 à 05:18, shiyi-pan notifications@github.com a écrit :

I fixed it by remove the full path in REFERENCE_GENOME and GENOME_SIZE

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shiyi-pan commented 4 years ago

hello  thank you for your reply.  I have fixed the error follwed your suggestion.Thank you very much.

------------------ 原始邮件 ------------------ 发件人: "AnthonyJaquaniello"<notifications@github.com>; 发送时间: 2020年3月4日(星期三) 下午5:10 收件人: "nservant/HiC-Pro"<HiC-Pro@noreply.github.com>; 抄送: "梦"<1343213784@qq.com>;"Author"<author@noreply.github.com>; 主题: Re: [nservant/HiC-Pro] error in install HiC-Pro-2.11.1 (#318)

Hello,

According to the documentation, REFERENCE_GENOME is just the genome prefix used for genome indexes, as hg19 for example. About GENOME_SIZE, the file is loaded from the ANNOTATION folder in the HiC-Pro installation directory, you just need to put the file name.

Le mer. 4 mars 2020 à 05:18, shiyi-pan <notifications@github.com> a écrit :

> I fixed it by remove the full path in REFERENCE_GENOME and GENOME_SIZE > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <https://github.com/nservant/HiC-Pro/issues/318?email_source=notifications&amp;email_token=ALHPTAOS3QGTWKUQBRE54BDRFXJANA5CNFSM4LAECVO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENWJESQ#issuecomment-594317898&gt;, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ALHPTAKQJUNWNGJGV55VK3LRFXJANANCNFSM4LAECVOQ&gt; > . >

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