Cannot import new SMRT Cells - pb-dyim/SMRT-Analysis GitHub Wiki

The assumed file structure needed to import SMRT Cells is a top-level-directory that contains the metadata.xml file and an "Analysis_Results" directory that contains the bas.h5 file.

A01_1
    m130227_052443_42141_c100505662540000001823074808081360_s1_p0.metadata.xml
    Analysis_Results
        m130227_052443_42141_c100505662540000001823074808081360_s1_p0.bas.h5
A01_2
    m130227_075201_42141_c100505662540000001823074808081361_s1_p0.metadata.xml
    Analysis_Results
        m130227_075201_42141_c100505662540000001823074808081361_s1_p0.bas.h5
B01_1    
    m130227_090546_42141_c100505662540000001823074808081362_s1_p0.metadata.xml
    m130227_090546_42141_c100505662540000001823074808081362_s2_p0.metadata.xml
    Analysis_Results
        m130227_090546_42141_c100505662540000001823074808081362_s1_p0.bas.h5
        m130227_090546_42141_c100505662540000001823074808081362_s2_p0.bas.h5

In this example, it is easy to tell that the sample in well A01 was sequenced using two SMRT Cells, and the results from each cell were placed in separate A01_1 and A01_2 directories. Each SMRT Cell was run with a single long movie as indicated by the s1 suffix. By contrast, the sample in well B01 was sequenced using two movies, producing two metadata.xml and bas.h5 files distinguished by s1 and s2 suffixes under the same B01_1 top level directory. The digit before the s1 suffix indicates the SMRT cell number in a given 8-pack. The sample in A01 was sequenced using the first (0_s1) and second (1_s1) SMRT cell, and the sample in B01 was sequenced using the third (2_s1) SMRT cell in the 8-pack.

Make sure the directory is in this file structure, and execute ls -l to make sure that the smrtanalysis user has read permissions to the files and execute permissions to the directories.