Missing pipeline binaries, file permissions are not set correctly, missing files, incorrectly formatted configuration files or insufficient memory
缺少管道二进制文件、文件权限设置不正确、文件丢失、配置文件格式不正确或内存不足
Ensure that executable binary files trimPhred, parseAlignment and countMutations are present in the ShapeMapper directory (see section on installing ShapeMapper). Check the log file (log.txt) in the run directory for details of the error. If running in a load-sharing facility–enabled cluster computing environment, also check the output of the submitted job, which will display errors due to file permissions or memory issues that cannot be captured in the ShapeMapper log file
确保 ShapeMapper 目录中存在可执行二进制文件 trimPhred、parseAlignment 和 countMutations（请参阅有关安装 ShapeMapper 的部分）。检查运行目录中的日志文件 （log.txt） 以获取错误的详细信息。如果在启用了负载共享设施的集群计算环境中运行，则还要检查已提交作业的输出，该作业将显示由于文件权限或内存问题而导致的错误，这些问题无法在 ShapeMapper 日志文件中捕获
Noisy reactivity profiles
嘈杂的反应性曲线
Incorrectly labeled samples, low read depths, poor signal above the background (low RNA modification rate or cDNA mutation rate in SHAPE-modified sample) or DNA contamination
样品标记错误、读取深度低、背景以上信号差（SHAPE 修饰样品中的 RNA 修饰率或 cDNA 突变率低）或 DNA 污染
Check the mutation rate and depth histograms in RUN/output/reactivity_profiles to determine the cause
检查 RUN/output/reactivity_profiles 中的突变率和深度直方图以确定原因
Missing samples
缺少样本
Unbalanced sequencing library sample loading or failed PCR
测序文库样本上样不平衡或PCR失败
Quantify missing samples with a high-sensitivity assay and re-sequence. Re-design directed primers if necessary. Increase the amount of RNA in reverse transcription and increase the amount of first-strand cDNA in PCR
使用高灵敏度检测对缺失样品进行定量，并重新测序。如有必要，重新设计定向引物。增加逆转录中RNA的量，增加PCR中第一链cDNA的量
Uneven read depth or regions of low depth
读取深度不均匀或深度低的区域
RNA degradation, poor primer binding or low RNA concentrationRNA
降解、引物结合不良或 RNA 浓度低
Sequence using longer reads; use Nextera kits (if using the Illumina platform); use more RNA in reverse transcription; and use a battery of paired PCR primers instead of random primers. For RNAs with regions of high AU content, consider using the LNA+ random primers (Fig. 6)
使用较长的读数进行排序;使用Nextera试剂盒（如果使用Illumina平台）;在逆转录中使用更多的RNA;并使用一组成对的PCR引物代替随机引物。对于具有高 AU 含量区域的 RNA，考虑使用 LNA+ 随机引物（图 6）
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No reactivity profiles are produced, even though alignment files (./output/aligned_reads/*.sam) are present
即使存在对齐文件 （./output/aligned_reads/*.sam），也不会生成反应性配置文件
Sample name(s) in the '[profiles]' section of the configuration file do not exactly match the name(s) given in the FASTA reference sequence files (.fa)
配置文件的“[profiles]”部分中的样本名称与 FASTA 参考序列文件 （.fa） 中给出的名称不完全匹配
Fix errors in the configuration file and rerun the generateReactivityProfiles stage
修复配置文件中的错误，并重新运行 generateReactivityProfiles 阶段
Pipeline run is incomplete, but there is no error message or an unhelpful error message in the log file
管道运行未完成，但日志文件中没有错误消息或无用的错误消息
Out-of-memory error or other error that ShapeMapper does not currently identify
内存不足错误或 ShapeMapper 当前无法识别的其他错误
Check the output from the ShapeMapper.py script itself, in addition to the log file (log.txt). Check the contents of the subfolders in the ./output/ directory in order of module execution (Table 2). The first folder in which some or all of the expected output files are missing, blank or empty indicates the stage that failed
除了日志文件 （log.txt） 之外，还要检查 ShapeMapper.py 脚本本身的输出。按照模块执行的顺序检查 ./output/ 目录中子文件夹的内容（表 2）。部分或全部预期输出文件丢失、空白或为空的第一个文件夹表示失败的阶段
表 7 SuperFold 故障排除表。
Step
Problem
Possible cause
Possible solution
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Error message: 'Program X not found in the path'
错误消息：“在路径中找不到程序 X”
RNAstructure command-line tools not available to SuperFoldRNAstructure
命令行工具不适用于 SuperFold
Make RNAstructure accessible by adding it to the shell path
通过将 RNAstructure 添加到 shell 路径中，使 RNAstructure 易于访问
Error message: 'DATAPATH not set...'
错误消息：“DATAPATH 未设置...”
RNAstructure DATAPATH is not set
未设置 RNAstructure DATAPATH
Use the export command to set the variable DATAPATH to the location of the RNAstructure data tables (see Supplementary Method 2)
使用 export 命令将变量 DATAPATH 设置为 RNAstructure 数据表的位置（请参阅补充方法 2）
Error message: 'Unexpected character in...'
错误消息：“意外字符在...”
Misformatted constraint
file格式错误的约束文件
Check the input files for extra spaces or special characters
检查输入文件中是否有多余的空格或特殊字符
Error message: 'pK region file incorrectly...'
错误消息：“pK 区域文件不正确...”
Misformatted constraint file
格式错误的约束文件
Check the pseudoknot constraint file for formatting. See the example file
检查伪结约束文件的格式设置。请参阅示例文件
No base pairs are found in the partition function
在分区函数中找不到碱基对
Crash in the program partition gives empty output
程序分区中的崩溃给出空输出
Set the–partitionWindowSize flag to 1200 and re-run SuperFold. Depending on the sequence, a large SHAPE penalty can cause the partition to malfunction with large window sizes将 –partitionWindowSize
标志设置为 1200，然后重新运行 SuperFold。根据顺序的不同，较大的 SHAPE 损失可能会导致分区在窗口大小较大的情况下发生故障
