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 codeError typeInterpretation
SAW-A00001Parameters invalid or missingPlease check your input parameters. Some required parameters might be missed.
SAW-A00002File open failedPlease check the input file exists and has the correct access permission.
SAW-A00003File parse failed

Please check your input file is in the correct file format.

e.g. "only support .bin or .h5 file."

SAW-A00004Other IO API errorPlease check your output directory path is an existing path.
e.g. "cannot write to file, /path/to/file"
SAW-A00021Parameters invalid or missingPlease check your input parameters. Some required parameters might be missed.
SAW-A00022File open failedPlease check the input file exists and has the correct access permission.
e.g. "cannot open such file, /path/to/file"
SAW-A00023Failed to parser the filePlease check your input file is in the correct file format.
SAW-A00024Other API errorPlease contact FAS/FBS for help.
SAW-A00025Software exceptionPlease contact FAS/FBS for help.
SAW-A10100Parameters invalid or missingThere is something wrong with the input FASTQs or --kit-version or --sequencing-type .
SAW-A10101File open failedPlease 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-A10102File parse failedPlease 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-A10103Invalid data or data exceptionPlease 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-A10105File IO failedPlease contact FAS/FBS for help.
SAW-A10106Failure on APIs of system and librariesPlease contact FAS/FBS for help.
SAW-A10107Software assertPlease contact FAS/FBS for help.
SAW-A10108Software exceptionPlease contact FAS/FBS for help.
SAW-A10109Allocate memory errorThis 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-A10110Out of disk spaceThis error occurs when you store too many files on your hard disk. Please remove some files to free disk space.
SAW-A10200Parameter missingPlease check your input parameters. Some required parameters might be missed.
SAW-A10201CID comparison rate is too lowThis 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-A10202Fail to create the index for the BAM filePlease contact FAS/FBS for help.
SAW-A10300Fail to load indexed referencePlease check the existence, access permission, and completeness for the indexed reference.
SAW-A12101Parameters invalid or missingPlease check your input parameters. Some required parameters might be missed.
SAW-A12102File open failedPlease check the input file that exists and has the correct access permission.
SAW-A12103File type invalidPlease check the file format.
SAW-A12104File parse failedPlease check your input file has a valid column number.
SAW-A12105Protein name invalid"PIDName" ONLY ACCEPTS letters [a-zA-Z], digits [0-9] and 4 symbols ["(", ")", "-", "_"].
SAW-A30001Arguments num errorPlease check your input parameters. Some required parameters might be missed.
SAW-A30002File open failedPlease check the input file exists and has the correct access permission.
SAW-A30003File parse failedPlease check your mask file is in the correct file format. Only support .h5 or .bin mask file.
SAW-A30004Allocate memory errorPlease 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-A30005Fail to open input fileFail to open input .txt file. Please check the file that exists and have the correct access permission.
SAW-A30007Run out of memoryPlease make you have preset enough memory resources for the task to run.

Annotation of reads

Error codeError typeInterpretation
SAW-A20001Parameter missingPlease check your input parameters. Some required parameters might be missed.
SAW-A20002File open failedPlease check the input file that exists and has the correct access permission.
SAW-A20003File parse failedPlease check your input BAM header is in the correct file format.
SAW-A20004Allocate memory errorThis 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-A20005File 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-A20101Parameter missingPlease check your input parameters. Some required parameters might be missed.
SAW-A20102File open failedPlease check the file that exists and has the correct access permission.
SAW-A20103File parse failedPlease check your input file has a valid column number.
SAW-A20105File 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-A20106Wrong file formatPlease check whether input file is in GTF/GFF format, suffixed with ( .gff/.gff.gz, .gff3/.gff3.gz, .gtf/.gft.gz)
SAW-A20107Abnormal file contentA gene ID matches multiple corresponding locations.
SAW-A20108Abnormal file contentDuplicate gene IDs appear in the same location on the same chromosome.

Image processing

Error codeError typeInterpretation
SAW-A40001Parameter missingPlease check your input parameters. Some required parameters might be missed.
SAW-A40002File open failedPlease check the input file that exists and has the correct access permission.
SAW-A40003File parse failedPlease check your input file is in the correct file format.
SAW-A40004Invalid data or data exceptionPlease check the file content.
SAW-A40401Parameter missingPlease check your SAW convert merge input parameters. Some required parameters might be missed.
SAW-A40402File open failedPlease check the SAW convert merge input file that exists and has the correct access permission.
SAW-A40405Invalid inputSAW convert merge inputs of less than two images or more than three images.
SAW-A40406File pairing failedPlease 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-A40501Parameter missingPlease check your SAW convert overlay input parameters. Some required parameters might be missed.
SAW-A40502File open failedPlease check the SAW convert overlay input file that exists and has the correct access permission.
SAW-A40504Invalid data or data exceptionError 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-A40601Parameter missingPlease check the SAW convert img2rpi input parameters. Some required parameters might be missed.
SAW-A40602File open failedPlease check the SAW convert img2rpi input file that exists and has the correct access permission.
SAW-A40605Invalid input--image and --layers of SAW convert img2rpi are not in the same length. They are supposed to be paired.
SAW-A40701Parameter missingPlease check the SAW convert img2rpi input parameters. Some required parameters might be missed.
SAW-A40702File open failedPlease check the SAW convert img2rpi input file that exists and has the correct access permission.
SAW-A40703File parse failedPlease check the input .tar.gz file from StereoMap.
SAW-A40704Invalid 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-A40706File pairing failedPlease check the shape of the registered tissue segmentation images. Or please contact FAS/FBS for help.
SAW-A40801Parameter missingPlease check your input parameters. Some required parameters might be missed.
SAW-A40802File open failedPlease check the file that exists and has the correct access permission.
SAW-A40803File parse failedPlease check your input file is in the correct file format.
SAW-A40804Invalid data or data exceptionPlease 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-A13001GEF parse failedPlease check the path or file format of GEF.
SAW-A13002TIFF parse failedPlease check the path or size of TIFF image.
SAW-A13003Fail to create outputPlease check the access permission to write files or whether the output directory exists.
SAW-A13004Invalid adjusting distancePlease check whether the adjusting distance is in a proper and reasonable range.

Expression matrix

Error codeError typeInterpretation
SAW-A50001Parameter missingPlease check your input parameters. Some required parameters might be missed.
SAW-A50002File open failedPlease check the file that exists and has the correct access permission.
SAW-A50003File parse failedPlease check your input file is in the correct file format.
SAW-A50004Fail to create output fileFail to create output file. Please check your writing permission of the output directory.
SAW-A50005Fail to write TIFFFail to write a TIFF file.
SAW-A50006h5AttrWrite errorPlease check the HDF5 file attributes.
SAW-A50007h5DatasetWrite errorPlease check the HDF5 file dataset.
SAW-A50008Fail to create TIFFPlease check the access permission to write a TIFF image.
SAW-A50009Different sizes between TIFF and GEFPlease check the sizes of the TIFF image and GEF respectively. Make sure they are the same size.
SAW-A50010Allocate memory errorThis 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-A60001Parameter missingPlease check your input parameters. Some required parameters might be missed.
SAW-A60002File open failedPlease check the file that exists and has the correct access permission.
SAW-A60003File parse failedThe file does not contain correct information. Please check the file format.
SAW-A60110Program version errorPlease check your output GEF version. Your input GEF version might be too old.
SAW-A60111Call process errorThis 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-A60120Invalid data or data exceptionError data. Please check the file content.
SAW-A60121File information missingFailed to read the file. Please check whether the file is damaged.
SAW-A60122File pairing failedPlease 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-A60130Fail to create output fileFail to create output H5 file. Please check your writing permission of the output directory or contact FAS/FBS for help.
SAW-A60140Allocate memory errorThis 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-A60150Abnormal file contentDimensions of gene expression matrix did not match. Please contact FAS/FBS for help.
SAW-A00031Parameters invalid or missingPlease check your input parameters. Some required parameters might be missed.
SAW-A00032File open failedPlease check the file that exists and has the correct access permission.
SAW-A00033File open failedPlease check the file format.
SAW-A00051Parameter InvalidPlease check your input parameters.
SAW-A00052File open failedNo such file or directory.
SAW-A00053File parse failedFile type error.
SAW-A00054Fail to create outputGenerate filtered gef failed.

Secondary analysis

Error codeError typeInterpretation
SAW-A70001Parameter missingPlease check your input parameters. Some required parameters might be missed.
SAW-A70002File open failedPlease check the file that exists and has the correct access permission.
e.g. “cannot access /path/to/file: No such file or directory.”
SAW-A70005Value 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-A70101Parameter missingPlease check your input parameters. Some required parameters might be missed.
SAW-A70102File open failedPlease check the file that exists and has the correct access permission.
e.g. “cannot access /path/to/file: No such file or directory.”
SAW-A70105Value 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-A14001Parameter InvalidPlease check your Transcriptomics GEF file.
SAW-A14002Parameter InvalidPlease check your Proteomics GEF file.
SAW-A14003Parameter InvalidPlease check your input binsize.
SAW-A14004Parameter InvalidPlease check your output directory.
SAW-A14005Invalid data or data exceptionGPU parameter is invalid, please check your input.
SAW-A14006Invalid data or data exceptionProtein panel and it is probably all filtered out.
SAW-A14007Invalid data or data exceptionRNA data and protein data are disjoint.
SAW-A14008Invalid data or data exceptionGenes to plot scatters are empty.

Report generation

Error codeError typeInterpretation
SAW-A80001Parameter missingPlease check your input parameters. Some required parameters might be missed.
SAW-A80002File open failedPlease check the file that exists and has the correct access permission.
SAW-A80003Abnormal file contentPlease check the content of input tissue GEF file.
SAW-A80004Abnormal file contentThere is no data left after filter by coordinates.
SAW-A80005Abnormal file contentTotal map reads is 0, please check the input statistic file.
SAW-A80006Abnormal file contentMapped reads are less than annotated reads.
SAW-A80007Environment errorPlotting error because of absence of python3.
SAW-A80008Programming error Fail to generate saturation file. Please contact FAS/FBS for help.
SAW-A90001Parameter missingPlease check your input parameter as prompted. Some required parameters might be missed.
SAW-A90002File open failedPlease check the file that exists and has the correct access permission.
e.g. "cannot access *: No such file or directory."
SAW-A90003File parse failedJSON 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-A90004Invalid data or data exceptionPlease check the file content. Fail to find the information of bin size or stain type in RPI file.
SAW-A90005Fail to create output fileFail to create output file. Please check your writing permission of the output directory.
SAW-A91001Parameter missingPlease check your input parameters. Some required parameters might be missed.
SAW-A91002File open failede.g. "cannot access *: No such file or directory."
SAW-A91004Invalid data or data exceptione.g. "information loss: fail to find 'bin_[size]' or 'ssDNA' in '*.rpi'."
SAW-A91005Fail to writee.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.

© 2025 STOmics Tech. All rights reserved.Modified: 2025-03-07 10:28:04

results matching ""

    No results matching ""