bamCoverage识别不了test.bam文件

$ bamCoverage -b test.bam -o test.bw
The file 'test.bam' does not have BAM or CRAM format

查看deeptools功能

$ deeptools
[ Tools for BAM and bigWig file processing ]
    multiBamSummary         compute read coverages over bam files. Output used for plotCorrelation or plotPCA
    multiBigwigSummary      extract scores from bigwig files. Output used for plotCorrelation or plotPCA
    correctGCBias           corrects GC bias from bam file. Don't use it with ChIP data
    bamCoverage             computes read coverage per bins or regions
    bamCompare              computes log2 ratio and other operations of read coverage of two samples per bins or regions
    bigwigCompare           computes log2 ratio and other operations from bigwig scores of two samples per bins or regions
    computeMatrix           prepares the data from bigwig scores for plotting with plotHeatmap or plotProfile

[ Tools for QC ]
    plotCorrelation         plots heatmaps or scatterplots of data correlation
    plotPCA                 plots PCA
    plotFingerprint         plots the distribution of enriched regions
    bamPEFragmentSize       returns the read length and paired-end distance from a bam file
    computeGCBias           computes and plots the GC bias of a sample
    plotCoverage            plots a histogram of read coverage

[Heatmaps and summary plots]
    plotHeatmap             plots one or multiple heatmaps of user selected regions over different genomic scores
    plotProfile             plots the average profile of user selected regions over different genomic scores
    plotEnrichment          plots the read/fragment coverage of one or more sets of regions

[Miscellaneous]
    computeMatrixOperations Modifies the output of computeMatrix in a variety of ways.

看起来，deeptools一切正常；

查看deeptools版本信息

$ deeptools --version

deepTools 3.0.2

重新安装deeptools

卸载deeptools，可以参考linux下python模块卸载

$ mkdir deepTools &&  cd deepTools  
$ git clone https://github.com/fidelram/deepTools ## 130M,
$ cd deepTools
$ python setup.py install --user
$ deeptools --version
deepTools 3.0.2
$ bamCoverage -b test.bam -o test.bw
The file 'test.bam' does not have BAM or CRAM format

问题还是没有解决，现在，我就考虑是不是版本的问题了；

$ sudo pip install deepTools==2.5.3
$ deeptools --version
deeptools 2.5.7
$ bamCoverage -b test.bam -o test.bw
test.bam does not appear to have an index. You MUST index the file first!
$ samtools index test.bam
$ bamCoverage -b test.bam -o test.bw

NOW，it’s ok!