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
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-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
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
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
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
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
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.
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