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Compile error for atac.bds #127

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DuYushen opened this issue Jun 26, 2018 · 1 comment
Open

Compile error for atac.bds #127

DuYushen opened this issue Jun 26, 2018 · 1 comment

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@DuYushen
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Hi,
Sorry it might be a naive question, but I cannot find a way to overcome it...
I am trying to install your pipeline. I think I have installed all required database/softwares, however, I got the following error when trying to run $bds atac.bds (I thought it should come up with the default parameters):
Compiler messages:
ERROR [ file 'atac.bds', line 1 ] : Class 'string' does not have memeber 'all_quality_metrics'
ERROR [ file 'atac.bds', line 1 ] : Expression 'title' is not an object
ERROR [ file 'atac.bds', line 1849 ] : Class 'null' does not have memeber 'tar'
ERROR [ file 'modules/align_bowtie2.bds', line 1 ] : Class 'string' does not have memeber 'csem'
ERROR [ file 'modules/align_bowtie2.bds', line 1 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/align_bowtie2.bds', line 1 ] : Class 'string' does not have memeber 'align'
ERROR [ file 'modules/align_bowtie2.bds', line 1 ] : Expression 'prefix2' is not an object
ERROR [ file 'modules/align_bowtie2.bds', line 1 ] : Class 'null' does not have memeber 'sorted'
ERROR [ file 'modules/align_bowtie2.bds', line 52 ] : Class 'string' does not have memeber 'bam'
ERROR [ file 'modules/align_bowtie2.bds', line 52 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/align_bowtie2.bds', line 53 ] : Class 'null' does not have memeber 'log'
ERROR [ file 'modules/align_bowtie2.bds', line 90 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/align_bowtie2.bds', line 90 ] : Class 'string' does not have memeber 'sam'
ERROR [ file 'modules/align_bowtie2.bds', line 91 ] : Class 'null' does not have memeber 'log'
ERROR [ file 'modules/align_bowtie2.bds', line 92 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/align_bowtie2.bds', line 93 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/align_bowtie2.bds', line 93 ] : Class 'string' does not have memeber 'csem'
ERROR [ file 'modules/align_bowtie2.bds', line 94 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/align_bowtie2.bds', line 134 ] : Class 'string' does not have memeber 'bam'
ERROR [ file 'modules/align_bowtie2.bds', line 134 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/align_bowtie2.bds', line 135 ] : Class 'null' does not have memeber 'log'
ERROR [ file 'modules/align_etc.bds', line 1 ] : Class 'string' does not have memeber 'read_length'
ERROR [ file 'modules/align_etc.bds', line 1 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/align_etc.bds', line 9 ] : Class 'null' does not have memeber 'txt'
ERROR [ file 'modules/align_trim_adapter.bds', line 1 ] : Class 'string' does not have memeber 'adapter'
ERROR [ file 'modules/align_trim_adapter.bds', line 1 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/align_trim_adapter.bds', line 1 ] : Class 'string' does not have memeber 'trim'
ERROR [ file 'modules/align_trim_adapter.bds', line 1 ] : Expression 'prefix2' is not an object
ERROR [ file 'modules/align_trim_adapter.bds', line 1 ] : Expression 'prefix1' is not an object
ERROR [ file 'modules/align_trim_adapter.bds', line 39 ] : Class 'null' does not have memeber 'txt'
ERROR [ file 'modules/align_trim_adapter.bds', line 119 ] : Class 'null' does not have memeber 'fastq'
ERROR [ file 'modules/align_trim_adapter.bds', line 120 ] : Class 'null' does not have memeber 'fastq'
ERROR [ file 'modules/align_trim_adapter.bds', line 121 ] : Class 'string' does not have memeber 'gz'
ERROR [ file 'modules/align_trim_adapter.bds', line 121 ] : Expression 'p1' is not an object
ERROR [ file 'modules/align_trim_adapter.bds', line 122 ] : Class 'string' does not have memeber 'gz'
ERROR [ file 'modules/align_trim_adapter.bds', line 122 ] : Expression 'p2' is not an object
ERROR [ file 'modules/align_trim_adapter.bds', line 157 ] : Expression 'p' is not an object
ERROR [ file 'modules/align_trim_adapter.bds', line 157 ] : Class 'string' does not have memeber 'gz'
ERROR [ file 'modules/align_trim_adapter.bds', line 159 ] : Expression 'p2' is not an object
ERROR [ file 'modules/align_trim_adapter.bds', line 159 ] : Class 'string' does not have memeber 'gz'
ERROR [ file 'modules/align_trim_adapter.bds', line 191 ] : Class 'null' does not have memeber 'fastq'
ERROR [ file 'modules/align_trim_adapter.bds', line 192 ] : Class 'null' does not have memeber 'fastq'
ERROR [ file 'modules/align_trim_adapter.bds', line 193 ] : Expression 'p1' is not an object
ERROR [ file 'modules/align_trim_adapter.bds', line 193 ] : Class 'string' does not have memeber 'gz'
ERROR [ file 'modules/align_trim_adapter.bds', line 194 ] : Class 'string' does not have memeber 'gz'
ERROR [ file 'modules/align_trim_adapter.bds', line 194 ] : Expression 'p2' is not an object
ERROR [ file 'modules/callpeak_bigbed.bds', line 1 ] : Expression 'bigbed' is not an object
ERROR [ file 'modules/callpeak_bigbed.bds', line 1 ] : Class 'string' does not have memeber 'chrsz'
ERROR [ file 'modules/callpeak_bigbed.bds', line 15 ] : Expression 'filetype' is not an object
ERROR [ file 'modules/callpeak_bigbed.bds', line 15 ] : Class 'string' does not have memeber 'bb'
ERROR [ file 'modules/callpeak_bigbed.bds', line 31 ] : Class 'null' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_bigbed.bds', line 32 ] : Expression 'bigbed' is not an object
ERROR [ file 'modules/callpeak_bigbed.bds', line 32 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_bigbed.bds', line 33 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_bigbed.bds', line 33 ] : Expression 'bigbed' is not an object
ERROR [ file 'modules/callpeak_bigbed.bds', line 33 ] : Class 'string' does not have memeber 'tmp2'
ERROR [ file 'modules/callpeak_bigbed.bds', line 33 ] : Class 'null' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_bigbed.bds', line 35 ] : Class 'string' does not have memeber 'tmp2'
ERROR [ file 'modules/callpeak_bigbed.bds', line 35 ] : Expression 'bigbed' is not an object
ERROR [ file 'modules/callpeak_bigbed.bds', line 35 ] : Class 'null' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_bigbed.bds', line 36 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_bigbed.bds', line 36 ] : Expression 'bigbed' is not an object
ERROR [ file 'modules/callpeak_bigbed.bds', line 36 ] : Class 'string' does not have memeber 'tmp2'
ERROR [ file 'modules/callpeak_bigbed.bds', line 36 ] : Class 'null' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_blacklist_filter.bds', line 16 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_blacklist_filter.bds', line 16 ] : Class 'string' does not have memeber 'filt'
ERROR [ file 'modules/callpeak_blacklist_filter.bds', line 16 ] : Class 'string' does not have memeber 'gz'
ERROR [ file 'modules/callpeak_blacklist_filter.bds', line 16 ] : Expression 'filetype' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 1 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 1 ] : Class 'string' does not have memeber 'FRiP'
ERROR [ file 'modules/callpeak_idr.bds', line 1 ] : Class 'real' does not have memeber 'narrowPeak'
ERROR [ file 'modules/callpeak_idr.bds', line 1 ] : Class 'real' does not have memeber 'filt'
ERROR [ file 'modules/callpeak_idr.bds', line 1 ] : Class 'real' does not have memeber 'log'
ERROR [ file 'modules/callpeak_idr.bds', line 1 ] : Expression 'idr_thresh' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 1 ] : Class 'null' does not have memeber 'narrowPeak'
ERROR [ file 'modules/callpeak_idr.bds', line 39 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 39 ] : Class 'string' does not have memeber 'IDR'
ERROR [ file 'modules/callpeak_idr.bds', line 39 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/callpeak_idr.bds', line 40 ] : Class 'string' does not have memeber 'IDR'
ERROR [ file 'modules/callpeak_idr.bds', line 40 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 41 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 41 ] : Class 'string' does not have memeber 'IDR'
ERROR [ file 'modules/callpeak_idr.bds', line 42 ] : Class 'string' does not have memeber 'IDR'
ERROR [ file 'modules/callpeak_idr.bds', line 42 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 42 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/callpeak_idr.bds', line 43 ] : Class 'string' does not have memeber 'IDR'
ERROR [ file 'modules/callpeak_idr.bds', line 43 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 43 ] : Class 'real' does not have memeber 'filt'
ERROR [ file 'modules/callpeak_idr.bds', line 43 ] : Expression 'idr_thresh' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 44 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 44 ] : Class 'string' does not have memeber 'IDR'
ERROR [ file 'modules/callpeak_idr.bds', line 44 ] : Expression 'idr_thresh' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 44 ] : Class 'real' does not have memeber 'filt'
ERROR [ file 'modules/callpeak_idr.bds', line 46 ] : Class 'string' does not have memeber 'unthresholded'
ERROR [ file 'modules/callpeak_idr.bds', line 46 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 47 ] : Class 'string' does not have memeber 'IDR'
ERROR [ file 'modules/callpeak_idr.bds', line 47 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 47 ] : Class 'null' does not have memeber 'txt'
ERROR [ file 'modules/callpeak_idr.bds', line 48 ] : Expression 'idr_out' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 48 ] : Class 'string' does not have memeber 'gz'
ERROR [ file 'modules/callpeak_idr.bds', line 49 ] : Class 'string' does not have memeber 'png'
ERROR [ file 'modules/callpeak_idr.bds', line 49 ] : Expression 'idr_out' is not an object
ERROR [ file 'modules/callpeak_idr.bds', line 117 ] : Class 'null' does not have memeber 'qc'
ERROR [ file 'modules/callpeak_idr.bds', line 152 ] : Class 'null' does not have memeber 'qc'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 1 ] : Class 'string' does not have memeber 'pval'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 1 ] : Class 'string' does not have memeber 'fc'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 1 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 1 ] : Class 'null' does not have memeber 'signal'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 1 ] : Expression 'prefix_sig' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 1 ] : Class 'null' does not have memeber 'srt'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 1 ] : Class 'string' does not have memeber 'broadPeak'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 1 ] : Expression 'cap_num_peak_macs2' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 1 ] : Class 'string' does not have memeber 'narrowPeak'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 1 ] : Class 'string' does not have memeber 'gappedPeak'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 51 ] : Class 'string' does not have memeber 'pval'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 51 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 51 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 53 ] : Class 'null' does not have memeber 'bedgraph'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 54 ] : Class 'null' does not have memeber 'bedgraph'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 55 ] : Class 'null' does not have memeber 'bigwig'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 57 ] : Class 'null' does not have memeber 'bedgraph'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 58 ] : Class 'null' does not have memeber 'bedgraph'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 59 ] : Class 'null' does not have memeber 'bigwig'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 85 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 85 ] : Expression 'peakfile' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 87 ] : Expression 'peakfile' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 87 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 88 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 88 ] : Expression 'peakfile' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 137 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 137 ] : Class 'string' does not have memeber 'pval'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 137 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 138 ] : Class 'string' does not have memeber 'pval'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 138 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 138 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 161 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 161 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 166 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 166 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 166 ] : Expression 'bpeakfile' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 167 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 167 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 167 ] : Expression 'gpeakfile' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 168 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 168 ] : Expression 'bpeakfile' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 169 ] : Expression 'gpeakfile' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 169 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 170 ] : Expression 'bpeakfile' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 170 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 170 ] : Expression 'gpeakfile' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 172 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 172 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 173 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 173 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 174 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 174 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 175 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 175 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 176 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/callpeak_macs2_atac.bds', line 176 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 1 ] : Class 'string' does not have memeber 'naive_overlap'
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 1 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 1 ] : Class 'string' does not have memeber 'filt_thru_npeak'
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 1 ] : Class 'null' does not have memeber 'gappedPeak'
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 33 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 33 ] : Class 'string' does not have memeber 'PooledInRep1AndRep2'
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 33 ] : Expression 'filetype' is not an object
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 33 ] : Class 'string' does not have memeber 'gz'
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 34 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 34 ] : Class 'string' does not have memeber 'naive_overlap'
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 34 ] : Class 'string' does not have memeber 'gz'
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 34 ] : Expression 'filetype' is not an object
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 35 ] : Expression 'filetype' is not an object
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 35 ] : Class 'string' does not have memeber 'gz'
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 35 ] : Class 'null' does not have memeber 'filt'
ERROR [ file 'modules/callpeak_naive_overlap.bds', line 217 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'adj'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'dupmark'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'nodup'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'flagstat'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'srt'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'nmsrt'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'tagAlign'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'fastq'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'filt'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'bedpe'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'rm_chr'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'qnmsrt'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'anon'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'dup'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Expression 'prefix2' is not an object
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'null' does not have memeber 'tagAlign'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Expression 'dupmark_bam' is not an object
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Expression 'tmp_filt_bam' is not an object
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'string' does not have memeber 'fixmate'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'null' does not have memeber 'pbc'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'null' does not have memeber 'flagstat'
ERROR [ file 'modules/postalign_bam.bds', line 1 ] : Class 'null' does not have memeber 'tmp'
ERROR [ file 'modules/postalign_bam.bds', line 84 ] : Class 'null' does not have memeber 'qc'
ERROR [ file 'modules/postalign_bam.bds', line 110 ] : Class 'string' does not have memeber 'bai'
ERROR [ file 'modules/postalign_bam.bds', line 110 ] : Expression 'bam' is not an object
ERROR [ file 'modules/postalign_bam.bds', line 132 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 133 ] : Class 'null' does not have memeber 'qc'
ERROR [ file 'modules/postalign_bam.bds', line 134 ] : Class 'null' does not have memeber 'qc'
ERROR [ file 'modules/postalign_bam.bds', line 135 ] : Class 'null' does not have memeber 'qc'
ERROR [ file 'modules/postalign_bam.bds', line 136 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 146 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 147 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 240 ] : Expression 'dupmark_bam' is not an object
ERROR [ file 'modules/postalign_bam.bds', line 240 ] : Class 'string' does not have memeber 'bai'
ERROR [ file 'modules/postalign_bam.bds', line 242 ] : Class 'string' does not have memeber 'bai'
ERROR [ file 'modules/postalign_bam.bds', line 242 ] : Expression 'filt_bam' is not an object
ERROR [ file 'modules/postalign_bam.bds', line 256 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 257 ] : Class 'null' does not have memeber 'qc'
ERROR [ file 'modules/postalign_bam.bds', line 258 ] : Class 'null' does not have memeber 'qc'
ERROR [ file 'modules/postalign_bam.bds', line 259 ] : Class 'null' does not have memeber 'qc'
ERROR [ file 'modules/postalign_bam.bds', line 260 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 270 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 296 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 308 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 310 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 365 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 367 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 371 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 382 ] : Class 'string' does not have memeber 'bai'
ERROR [ file 'modules/postalign_bam.bds', line 382 ] : Expression 'dupmark_bam' is not an object
ERROR [ file 'modules/postalign_bam.bds', line 384 ] : Class 'string' does not have memeber 'bai'
ERROR [ file 'modules/postalign_bam.bds', line 384 ] : Expression 'filt_bam' is not an object
ERROR [ file 'modules/postalign_bam.bds', line 397 ] : Class 'null' does not have memeber 'qc'
ERROR [ file 'modules/postalign_bam.bds', line 398 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 455 ] : Class 'null' does not have memeber 'qc'
ERROR [ file 'modules/postalign_bam.bds', line 456 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 474 ] : Class 'string' does not have memeber 'bai'
ERROR [ file 'modules/postalign_bam.bds', line 474 ] : Expression 'dupmark_bam' is not an object
ERROR [ file 'modules/postalign_bam.bds', line 487 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 515 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 543 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 584 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bam.bds', line 586 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bam.bds', line 617 ] : Class 'null' does not have memeber 'bam'
ERROR [ file 'modules/postalign_bam.bds', line 618 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bam.bds', line 657 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bam.bds', line 660 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bam.bds', line 692 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bam.bds', line 695 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bam.bds', line 730 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bam.bds', line 764 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bam.bds', line 798 ] : Class 'string' does not have memeber 'png'
ERROR [ file 'modules/postalign_bam.bds', line 798 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/postalign_bam.bds', line 799 ] : Class 'string' does not have memeber 'qc'
ERROR [ file 'modules/postalign_bam.bds', line 799 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/postalign_bed.bds', line 1 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/postalign_bed.bds', line 1 ] : Class 'string' does not have memeber 'joined'
ERROR [ file 'modules/postalign_bed.bds', line 1 ] : Class 'string' does not have memeber 'tn5'
ERROR [ file 'modules/postalign_bed.bds', line 1 ] : Expression 'prefix_pr2' is not an object
ERROR [ file 'modules/postalign_bed.bds', line 1 ] : Class 'string' does not have memeber 'pr1'
ERROR [ file 'modules/postalign_bed.bds', line 1 ] : Class 'null' does not have memeber 'tagAlign'
ERROR [ file 'modules/postalign_bed.bds', line 1 ] : Expression 'prefix_pr1' is not an object
ERROR [ file 'modules/postalign_bed.bds', line 1 ] : Class 'string' does not have memeber 'pr2'
ERROR [ file 'modules/postalign_bed.bds', line 1 ] : Class 'string' does not have memeber 'tagAlign'
ERROR [ file 'modules/postalign_bed.bds', line 1 ] : Expression 'nreads_per_mill' is not an object
ERROR [ file 'modules/postalign_bed.bds', line 34 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bed.bds', line 69 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bed.bds', line 73 ] : Class 'string' does not have memeber 'joined'
ERROR [ file 'modules/postalign_bed.bds', line 73 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/postalign_bed.bds', line 74 ] : Class 'null' does not have memeber 'subsampled'
ERROR [ file 'modules/postalign_bed.bds', line 116 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bed.bds', line 146 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bed.bds', line 147 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bed.bds', line 181 ] : Function add_task_to_graph(string[],string[],string[]) cannot be resolved
ERROR [ file 'modules/postalign_bed.bds', line 191 ] : Expression 'prefix_pr1' is not an object
ERROR [ file 'modules/postalign_bed.bds', line 191 ] : Class 'string' does not have memeber 'joined'
ERROR [ file 'modules/postalign_bed.bds', line 193 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bed.bds', line 194 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bed.bds', line 235 ] : Function add_task_to_graph(string[],string[],string[]) cannot be resolved
ERROR [ file 'modules/postalign_bed.bds', line 245 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_bed.bds', line 279 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_xcor.bds', line 1 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/postalign_xcor.bds', line 1 ] : Class 'string' does not have memeber 'joined'
ERROR [ file 'modules/postalign_xcor.bds', line 1 ] : Class 'string' does not have memeber 'cc'
ERROR [ file 'modules/postalign_xcor.bds', line 1 ] : Class 'null' does not have memeber 'plot'
ERROR [ file 'modules/postalign_xcor.bds', line 1 ] : Expression 'nreads_per_mill' is not an object
ERROR [ file 'modules/postalign_xcor.bds', line 1 ] : Class 'string' does not have memeber 'R1'
ERROR [ file 'modules/postalign_xcor.bds', line 1 ] : Class 'null' does not have memeber 'tagAlign'
ERROR [ file 'modules/postalign_xcor.bds', line 44 ] : Class 'null' does not have memeber 'gz'
ERROR [ file 'modules/postalign_xcor.bds', line 47 ] : Class 'string' does not have memeber 'joined'
ERROR [ file 'modules/postalign_xcor.bds', line 47 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/postalign_xcor.bds', line 48 ] : Class 'null' does not have memeber 'subsampled'
ERROR [ file 'modules/postalign_xcor.bds', line 89 ] : Class 'null' does not have memeber 'qc'
ERROR [ file 'modules/postalign_xcor.bds', line 90 ] : Class 'null' does not have memeber 'pdf'
ERROR [ file 'modules/postalign_xcor.bds', line 116 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/postalign_xcor.bds', line 116 ] : Expression 'xcor_score' is not an object
ERROR [ file 'modules/postalign_xcor.bds', line 117 ] : Expression 'xcor_score' is not an object
ERROR [ file 'modules/postalign_xcor.bds', line 117 ] : Class 'string' does not have memeber 'tmp'
ERROR [ file 'modules/report.bds', line 443 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/report.bds', line 443 ] : Class 'string' does not have memeber 'hammock'
ERROR [ file 'modules/report.bds', line 444 ] : Expression 'prefix' is not an object
ERROR [ file 'modules/report.bds', line 444 ] : Class 'string' does not have memeber 'tmp'

Can you please help me with this issue ? Thank you soooo much !!!
@leepc12
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leepc12 commented Jun 26, 2018

$ bds atac.bds will just show help. Please check if you installed BDS (forked) correctly.
https://github.com/kundajelab/atac_dnase_pipelines#bigdatascript

Also, the pipeline itself https://github.com/kundajelab/atac_dnase_pipelines#pipeline

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@leepc12 @DuYushen