Troubleshooting

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 .bin or .h5 file."
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-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.

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.

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.

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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.