错误码
*The interpretation of the Error Code part is only available in EN.
Error codes
Under the execution directory, a file named errcode.log will record the error information of pipelines if an error causes a program interruption. Offer the errcode.log and pipeline log to the FAS/FBS for help.
SAW error codes are designed to capture error information and describe it in a straightforward manner. They are designed to express in three parts, date-time, error code, and explanation. The date-time information could help users distinguish errors in various program executions.
An empty errcode.log file will be generated if the pipeline runs successfully.
According to the workflow, error codes for each step are listed below.
Alignment of reads
| Error code | Error type | Interpretation |
|---|---|---|
| SAW-A00001 | Parameters invalid or missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A00002 | File open failed | Please check the input file exists and has the correct access permission. |
| SAW-A00003 | File parse failed | Please check your input file is in the correct file format. e.g. "only support |
| SAW-A00004 | Other IO API error | Please check your output directory path is an existing path. e.g. "cannot write to file, /path/to/file" |
| SAW-A00021 | Parameters invalid or missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A00022 | File open failed | Please check the input file exists and has the correct access permission. e.g. "cannot open such file, /path/to/file" |
| SAW-A00023 | Failed to parser the file | Please check your input file is in the correct file format. |
| SAW-A00024 | Other API error | Please contact FAS/FBS for help. |
| SAW-A00025 | Software exception | Please contact FAS/FBS for help. |
| SAW-A10100 | Parameters invalid or missing | There is something wrong with the input FASTQs or --kit-version or --sequencing-type . |
| SAW-A10101 | File open failed | Please check the file permission and file format. e.g. "barcodePositionMapFile does not exist: /path/to/mask" means to check whether the mask file exists and has the correct access permission. |
| SAW-A10102 | File parse failed | Please check the completeness of the reads in FASTQs. This issue may arise if the FASTQs are in incorrect format or the file was incompletely written or transferred. e.g. "sequence and quality have different length" |
| SAW-A10103 | Invalid data or data exception | Please check the file format and content. |
| SAW-A10104 | File deletion failed | Please check whether the program has finished according to the *.Log.progress.out or *.run.log file. This error arose if "_STARtmp" directory failed to be deleted. |
| SAW-A10105 | File IO failed | Please contact FAS/FBS for help. |
| SAW-A10106 | Failure on APIs of system and libraries | Please contact FAS/FBS for help. |
| SAW-A10107 | Software assert | Please contact FAS/FBS for help. |
| SAW-A10108 | Software exception | Please contact FAS/FBS for help. |
| SAW-A10109 | Allocate memory error | This error occurs when you run out of RAM. You may need to kill some jobs that use the same RAM or upgrade your hardware to get more RAM resources for your job. |
| SAW-A10110 | Out of disk space | This error occurs when you store too many files on your hard disk. Please remove some files to free disk space. |
| SAW-A10200 | Parameter missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A10201 | CID comparison rate is too low | This error usually arises because the CID information of the input FASTQs is not the same as the CID in the input mask file. Please use the correct SN-FASTQ pairs for SAW count. |
| SAW-A10202 | Fail to create the index for the BAM file | Please contact FAS/FBS for help. |
| SAW-A10300 | Fail to load indexed reference | Please check the existence, access permission, and completeness for the indexed reference. |
| SAW-A12101 | Parameters invalid or missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A12102 | File open failed | Please check the input file that exists and has the correct access permission. |
| SAW-A12103 | File type invalid | Please check the file format. |
| SAW-A12104 | File parse failed | Please check your input file has a valid column number. |
| SAW-A12105 | Protein name invalid | "PIDName" ONLY ACCEPTS letters [a-zA-Z], digits [0-9] and 4 symbols ["(", ")", "-", "_"]. |
| SAW-A30001 | Arguments num error | Please check your input parameters. Some required parameters might be missed. |
| SAW-A30002 | File open failed | Please check the input file exists and has the correct access permission. |
| SAW-A30003 | File parse failed | Please check your mask file is in the correct file format. Only support .h5 or .bin mask file. |
| SAW-A30004 | Allocate memory error | Please check whether the range of the coordinates is too large, or you have run out of RAM. You may need to kill some jobs that use the same RAM or upgrade your hardware to get more RAM resources for your job. |
| SAW-A30005 | Fail to open input file | Fail to open input .txt file. Please check the file that exists and have the correct access permission. |
| SAW-A30007 | Run out of memory | Please make you have preset enough memory resources for the task to run. |
Annotation of reads
| Error code | Error type | Interpretation |
|---|---|---|
| SAW-A20001 | Parameter missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A20002 | File open failed | Please check the input file that exists and has the correct access permission. |
| SAW-A20003 | File parse failed | Please check your input BAM header is in the correct file format. |
| SAW-A20004 | Allocate memory error | This error occurs when you run out of RAM. You may need to kill some jobs that use the same RAM or upgrade your hardware to get more RAM resources for your job. |
| SAW-A20005 | File parse failed | Please check gene names in your input GTF/GFF file. e.g. "Found <number> gene names with their length exceeding 64 characters" |
| SAW-A20101 | Parameter missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A20102 | File open failed | Please check the file that exists and has the correct access permission. |
| SAW-A20103 | File parse failed | Please check your input file has a valid column number. |
| SAW-A20105 | File parse failed | Please check gene names in your input GTF/GFF file. e.g. "Found <number> gene names with their length exceeding 64 characters" |
| SAW-A20106 | Wrong file format | Please check whether input file is in GTF/GFF format, suffixed with ( .gff/.gff.gz, .gff3/.gff3.gz, .gtf/.gft.gz） |
| SAW-A20107 | Abnormal file content | A gene ID matches multiple corresponding locations. |
| SAW-A20108 | Abnormal file content | Duplicate gene IDs appear in the same location on the same chromosome. |
Image processing
| Error code | Error type | Interpretation |
|---|---|---|
| SAW-A40001 | Parameter missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A40002 | File open failed | Please check the input file that exists and has the correct access permission. |
| SAW-A40003 | File parse failed | Please check your input file is in the correct file format. |
| SAW-A40004 | Invalid data or data exception | Please check the file content. |
| SAW-A40401 | Parameter missing | Please check your SAW convert merge input parameters. Some required parameters might be missed. |
| SAW-A40402 | File open failed | Please check the SAW convert merge input file that exists and has the correct access permission. |
| SAW-A40405 | Invalid input | SAW convert merge inputs of less than two images or more than three images. |
| SAW-A40406 | File pairing failed | Please check the SAW convert merge input TIFF sizes are the same. Since the merge function is used for evaluating segmentation results, the input images are supposed to be the same in size and position (tissue position in the whole image). |
| SAW-A40501 | Parameter missing | Please check your SAW convert overlay input parameters. Some required parameters might be missed. |
| SAW-A40502 | File open failed | Please check the SAW convert overlay input file that exists and has the correct access permission. |
| SAW-A40504 | Invalid data or data exception | Error data. Please check the file content. This error may arise because the IPR file in the image .tar.gz does not contain 'Stitch/TransformTemplate' or 'Register/MatrixTemplate information'. |
| SAW-A40601 | Parameter missing | Please check the SAW convert img2rpi input parameters. Some required parameters might be missed. |
| SAW-A40602 | File open failed | Please check the SAW convert img2rpi input file that exists and has the correct access permission. |
| SAW-A40605 | Invalid input | --image and --layers of SAW convert img2rpi are not in the same length. They are supposed to be paired. |
| SAW-A40701 | Parameter missing | Please check the SAW convert img2rpi input parameters. Some required parameters might be missed. |
| SAW-A40702 | File open failed | Please check the SAW convert img2rpi input file that exists and has the correct access permission. |
| SAW-A40703 | File parse failed | Please check the input .tar.gz file from StereoMap. |
| SAW-A40704 | Invalid data or data exception | Please check the SAW convert img2rpi input .tar.gz file. This error may arise because the CZI file in .tar.gz is invalid, or the image has not been either automatically or manually registered with the expression matrix. |
| SAW-A40706 | File pairing failed | Please check the shape of the registered tissue segmentation images. Or please contact FAS/FBS for help. |
| SAW-A40801 | Parameter missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A40802 | File open failed | Please check the file that exists and has the correct access permission. |
| SAW-A40803 | File parse failed | Please check your input file is in the correct file format. |
| SAW-A40804 | Invalid data or data exception | Please check the file content. This error may arise because the input file is empty. The second possible reason is that the gene expression matrix information in the Register module (MatrixShape, Xstart, Ystart) does not match with the input GEF file (minX, minY, maxX, maxY), because the manual registration has to be processed on the identical matrix. |
| SAW-A13001 | GEF parse failed | Please check the path or file format of GEF. |
| SAW-A13002 | TIFF parse failed | Please check the path or size of TIFF image. |
| SAW-A13003 | Fail to create output | Please check the access permission to write files or whether the output directory exists. |
| SAW-A13004 | Invalid adjusting distance | Please check whether the adjusting distance is in a proper and reasonable range. |
Expression matrix
| Error code | Error type | Interpretation |
|---|---|---|
| SAW-A50001 | Parameter missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A50002 | File open failed | Please check the file that exists and has the correct access permission. |
| SAW-A50003 | File parse failed | Please check your input file is in the correct file format. |
| SAW-A50004 | Fail to create output file | Fail to create output file. Please check your writing permission of the output directory. |
| SAW-A50005 | Fail to write TIFF | Fail to write a TIFF file. |
| SAW-A50006 | h5AttrWrite error | Please check the HDF5 file attributes. |
| SAW-A50007 | h5DatasetWrite error | Please check the HDF5 file dataset. |
| SAW-A50008 | Fail to create TIFF | Please check the access permission to write a TIFF image. |
| SAW-A50009 | Different sizes between TIFF and GEF | Please check the sizes of the TIFF image and GEF respectively. Make sure they are the same size. |
| SAW-A50010 | Allocate memory error | This error occurs when you run out of RAM. You may need to kill some jobs that use the same RAM or upgrade your hardware to get more RAM resources for your job. |
| SAW-A60001 | Parameter missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A60002 | File open failed | Please check the file that exists and has the correct access permission. |
| SAW-A60003 | File parse failed | The file does not contain correct information. Please check the file format. |
| SAW-A60110 | Program version error | Please check your output GEF version. Your input GEF version might be too old. |
| SAW-A60111 | Call process error | This error arose because the invocation flow order was messed up. Please modify your invocation flow as prompted. e.g. "Please call freeRestriction first, or call restrictRegion function before restrictGene." |
| SAW-A60120 | Invalid data or data exception | Error data. Please check the file content. |
| SAW-A60121 | File information missing | Failed to read the file. Please check whether the file is damaged. |
| SAW-A60122 | File pairing failed | Please check the TIFF mask size is consistent with the size of expression matrix. Since the mask has been registered with the expression matrix, their sizes are supposed to be the same. |
| SAW-A60130 | Fail to create output file | Fail to create output H5 file. Please check your writing permission of the output directory or contact FAS/FBS for help. |
| SAW-A60140 | Allocate memory error | This error occurs when you run out of RAM. You may need to kill some jobs that use the same RAM or upgrade your hardware to get more RAM resources for your job. |
| SAW-A60150 | Abnormal file content | Dimensions of gene expression matrix did not match. Please contact FAS/FBS for help. |
| SAW-A00031 | Parameters invalid or missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A00032 | File open failed | Please check the file that exists and has the correct access permission. |
| SAW-A00033 | File open failed | Please check the file format. |
| SAW-A00051 | Parameter Invalid | Please check your input parameters. |
| SAW-A00052 | File open failed | No such file or directory. |
| SAW-A00053 | File parse failed | File type error. |
| SAW-A00054 | Fail to create output | Generate filtered gef failed. |
Secondary analysis
| Error code | Error type | Interpretation |
|---|---|---|
| SAW-A70001 | Parameter missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A70002 | File open failed | Please check the file that exists and has the correct access permission. e.g. “cannot access /path/to/file: No such file or directory.” |
| SAW-A70005 | Value error | Please reset the bin size as prompted. e.g. "Gene number less than 3000, please check your gef file"Please check the content of your GEF file, and make sure there are at least 3000 genes for clustering. |
| SAW-A70101 | Parameter missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A70102 | File open failed | Please check the file that exists and has the correct access permission. e.g. “cannot access /path/to/file: No such file or directory.” |
| SAW-A70105 | Value error | Please reset the bin size as prompted. e.g. "Gene number less than 3000, please check your gef file"Please check the content of your GEF file, and make sure there are at least 3000 genes for clustering. |
| SAW-A14001 | Parameter Invalid | Please check your Transcriptomics GEF file. |
| SAW-A14002 | Parameter Invalid | Please check your Proteomics GEF file. |
| SAW-A14003 | Parameter Invalid | Please check your input binsize. |
| SAW-A14004 | Parameter Invalid | Please check your output directory. |
| SAW-A14005 | Invalid data or data exception | GPU parameter is invalid, please check your input. |
| SAW-A14006 | Invalid data or data exception | Protein panel and it is probably all filtered out. |
| SAW-A14007 | Invalid data or data exception | RNA data and protein data are disjoint. |
| SAW-A14008 | Invalid data or data exception | Genes to plot scatters are empty. |
Report generation
| Error code | Error type | Interpretation |
|---|---|---|
| SAW-A80001 | Parameter missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A80002 | File open failed | Please check the file that exists and has the correct access permission. |
| SAW-A80003 | Abnormal file content | Please check the content of input tissue GEF file. |
| SAW-A80004 | Abnormal file content | There is no data left after filter by coordinates. |
| SAW-A80005 | Abnormal file content | Total map reads is 0, please check the input statistic file. |
| SAW-A80006 | Abnormal file content | Mapped reads are less than annotated reads. |
| SAW-A80007 | Environment error | Plotting error because of absence of python3. |
| SAW-A80008 | Programming error | Fail to generate saturation file. Please contact FAS/FBS for help. |
| SAW-A90001 | Parameter missing | Please check your input parameter as prompted. Some required parameters might be missed. |
| SAW-A90002 | File open failed | Please check the file that exists and has the correct access permission. e.g. "cannot access *: No such file or directory." |
| SAW-A90003 | File parse failed | JSON file format error. This error may arise because the input statistics files were not generated in the same SAW version. Or contact FAS/FBS for help. |
| SAW-A90004 | Invalid data or data exception | Please check the file content. Fail to find the information of bin size or stain type in RPI file. |
| SAW-A90005 | Fail to create output file | Fail to create output file. Please check your writing permission of the output directory. |
| SAW-A91001 | Parameter missing | Please check your input parameters. Some required parameters might be missed. |
| SAW-A91002 | File open failed | e.g. "cannot access *: No such file or directory." |
| SAW-A91004 | Invalid data or data exception | e.g. "information loss: fail to find 'bin_[size]' or 'ssDNA' in '*.rpi'." |
| SAW-A91005 | Fail to write | e.g. "failed to write in html" or "failed to write final_result_json." |
Access to help
Have any questions or concerns about the error codes fromyour SAW run?
Please get in touch with the local agents or FAS/FBS.