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SAW Software Operation Manual SAW Software Operation Manual
SAW Software Operation Manual
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SAW operation manual
Appendices and References
Appendix A: Recommended Directory Structure for Raw Data
Recommend to organize raw data as below if users prefer to use SAW shell script provided on the SAW GitHub page (https://github.com/STOmics/SAW).
$ tree
.
|-- image
|   |-- SS200000135TL_D1_20220527_201353_1.1.0.ipr
|   `-- SS200000135TL_D1_20220527_201353_1.1.0.tar.gz
|-- mask
|   `-- SS200000135TL_D1.barcodeToPos.h5
|-- md5
|-- reads
|   |-- E100026571_L01_trim_read_1.fq.gz
|   `-- E100026571_L01_trim_read_2.fq.gz
`-- reference
    |-- STAR_SJ100
    |   |-- Genome
    |   |-- SA
    |   |-- SAindex
    |   |-- chrLength.txt
    |   |-- chrName.txt
    |   |-- chrNameLength.txt
    |   |-- chrStart.txt
    |   |-- exonGeTrInfo.tab
    |   |-- exonInfo.tab
    |   |-- geneInfo.tab
    |   |-- genomeParameters.txt
    |   |-- genomeParameters_bkp.txt
    |   |-- sjdbInfo.txt
    |   |-- sjdbList.fromGTF.out.tab
    |   |-- sjdbList.out.tab
    |   `-- transcriptInfo.tab
    |-- genes.gtf
    `-- genome.fa
 
5 directories, 24 files
Appendix B: SAW ST Output File List
step
output
File Description
splitMask
*.SN.barcodeToPos.bin
Split Stereo-seq Chip T mask file according to the CID.
mapping
lane.Aligned.sortedByCoord.out.bam
Binary Alignment/Map file, used for storing the sequence alignment information.
lane.Aligned.sortedByCoord.out.bam.csi
BAM index file, which is a table of contents for the BAM file that indicating where in the BAM file a specific read of set of reads can be found.
lane.barcodeReadsCount.txt
BMapped CID list file with reads counts for each CID, the three columns record x, y, and read count.
lane.Log.final.out
Summary mapping statistics after mapping job is complete (STAR output).
lane.Log.out
Main log file in STAR mapping (STAR output).
lane.Log.progress.out
Reports job process statistics (STAR output).
lane.SJ.out.tab
Splice junctions detected in the mapping (STAR output).
lane.bcPara
A parameters file defines CID mapping options.
mapping
lane_barcodeMap.stat
Statistical report of CID mapping, such as CID mapped reads count, reads sequencing quality, mapped DNB count, etc.
merge
SN.barcodeReadsCount.txt
Mapped CID list file with reads counts for each CID., the three columns record x, y, and read count.

SN.Aligned.sortedByCoord.out.merge.

q10.dedup.target.bam

Annotated BAM file sorted by coordinate, includes uniquely mapped reads and multi-mapped reads whose HI:i tag is 1.

SN.Aligned.sortedByCoord.out.merge.

q10.dedup.target.bam.csi

Index file of annotated BAM.

SN.Aligned.sortedByCoord.out.merge.

q10.dedup.target.bam.summary.stat

Statistical summary report file for count. Total reads in filter&deduplication metrics stand for the total alignment record count in BAM. Pass filter and total reads in annotation metrics are the same, they represent uniquely mapped reads that will be used for annotation, MID correction and quantification.
SN.raw.gef
Gene expression file in hdf5 format. This is the first raw matrix that includes the expression information over a complete chip region. It only includes geneExp group for the bin size of 1. The origin of expression matrix has been calibrated to (0,0), and the offset x and y has been record as minX and minY in the attribute of geneExp/expression dataset.
count
SN_raw_barcode_gene_exp.txt
A space-separate file records coordinate, gene, MID, and count information. Which is prepared to be a sampling file that performs sequence saturation. The 5 columns are y, x, geneIndex, MIDIndex, readCount.
date-hh-mm-ss.log
Log file.
attrs.json
Height and width of gene expression matrix.

SN or other user specified name for the 

image folder used when input into 

imageQC/imageStudio

This subdirectory stores raw small image pieces in TIFF format.
SN_0000_0000_YYYY-MM-DD_hh-mm-ss-n.tif
Small image pieces in TIFF format.
fov_stitched_transformed.tif
The stitched panoramic image that has pre-registered with the track line pattern template. So that it will not need to further rotate a non-right angle or scale.
matrix_template.txt
Track line cross point template for the registered ssDNA image. Used for assessing registeration result.
SN_date_time_version.ipr
IPR format image process record file which records basic image information gathered from imageQC/imageStudio.
SN_mask.tif
Registered cell segmentation binary image file in TIFF format.
SN_regist.tif
Registered panoramic image file in TIFF format.
SN.rpi
Registered panoramic image file, tissue area boundary, and cell boundaries (downsampled) that stores as an image pyramid.
SN_tissue_bbox.csv
Registered panoramic image size.
SN_tissue_cut.tif
The tissue segmentation result of registered panoramic image file in TIFF format.
register &  imageTools ipr2img
transform_template.txt
Track line cross point template for the fov_stitched_transformed.tif. Used for assessing stitching result.
transform_thumb.png
A downsampled pre-registered panoramic image.
SN.gef
A gene expression file in hdf5 format. This file is a complete GEF format which includes geneExp group and wholeExp group in bin1, 10, 20, 50, 100, 200, and 500. It also includes a stat group. The origin of expression matrix has been calibrated to (0,0), and the offset x and y has been recorded as minX and minY in the attribute of geneExp/expression dataset.
SN.tissue.gef
A gene expression file in hdf5 format. Tissue GEF includes the expression information of the tissue coverage region. It only includes geneExp group for the bin size of 1. The origin of expression matrix has been calibrated to (0,0), and the offset x and y has been recorded as minX and minY in the attribute of geneExp/expression dataset same to raw GEF.
tissue_fig
This directory stores the statistical plots for the tissue coverage region
scatter_100x100_MID_gene_counts.png
Scatter plot of MID count and gene number in each bin (bin100)
scatter_150x150_MID_gene_counts.png
Scatter plot of MID count and gene number in each bin (bin150)
scatter_200x200_MID_gene_counts.png
Scatter plot of MID count and gene number in each bin (bin200)
scatter_50x50_MID_gene_counts.png
Scatter plot of MID count and gene number in each bin (bin50)
statistic_100x100_MID_gene_DNB.png
Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis (bin100)
statistic_150x150_MID_gene_DNB.png
Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis (bin150)
statistic_200x200_MID_gene_DNB.png
Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis (bin200)
statistic_50x50_MID_gene_DNB.png
Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis (bin50)
violin_100x100_MID_gene.png
Violin plots show the distribution of deduplicated MID count and gene number in each bin (bin100)
violin_150x150_MID_gene.png
Violin plots show the distribution of deduplicated MID count and gene number in each bin (bin150)
violin_200x200_MID_gene.png
Violin plots show the distribution of deduplicated MID count and gene number in each bin (bin200)
violin_50x50_MID_gene.png
Violin plots show the distribution of deduplicated MID count and gene number in each bin (bin50)
tissuecut.stat
Statistical report for tissue coverage region.
SN.cellbin.gef
A gene expression file for cells in hdf5 format. Cellbin GEF includes the expression information of the cells, such as the coordinate of the centroid, boundary coordinates, expression of genes, and cell area. The cell is record by its boundary. The origin of expression matrix has been calibrated to (0,0), and the coordinate offset x and y has been record as offsetX and offsetY in the attribute of the GEF file same to minX and minY in the raw GEF file.
SN.spatial.cluster.h5ad
H5AD file for spatial clustering analysis result.
SN.cell.cluster.h5ad
H5AD file for cell clustering analysis result.
saturation
plot_1x1_saturation.png
Sequencing saturation analysis plots for bin1. Calculated by 1- (unique reads/total reads) for each bin (bin1).
saturation
plot_200x200_saturation.png
Sequencing saturation analysis plots for bin200. Calculated by 1- (unique reads/total reads) for each bin (bin1).
saturation
sequence_saturation.tsv
Sequence saturation file. The nine colums are sampling component (#sample), bin1 total reads (bar_x), sequence saturation value at bin1 (bar_y1), median gene count at bin1 (bar_y2), unique reads at bin1 (bar_umi), bin200 total reads (bin_x), sequence saturation value at bin200 (bin_y1), median gene count at bin200 (bin_y2), and unique reads at bin200 (bin_umi), respectively.
report
SN.report.html
HTML analytical report.
SN.statistics.json
Statistical summary report in JSON format. It gathers all important statistical metrics from the statistical report in each step.
scatter_1x1_MID_gene_counts.png
Scatter plot of MID count and gene number in each cell
report
statistic_1x1_MID_gene_DNB.png
Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis of each cell
violin_1x1_MID_gene.png
Violin plots show the distribution of deduplicated MID count and gene number in each cell
Appendix C: Handling Errors and Exceptions Common Errors
Common Errors
  • File access error:
  • Some examples of file access error:
terminate called after throwing an instance of 'std::invalid_argument'
what():  Could not open the file: xxxxxx
...
Or
#006: H5FDsec2.c line 352 in H5FD__sec2_open(): unable to open file: name = '/path/to/hdf5/file', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0
    major: File accessibility
    minor: Unable to open file
...
Solution:
# Attempt 1: Bind file path before execute command.
$ export SINGULARITY_BIND="/path/to/file/directory"

# Attempt 2: Turn off the HDF5 lock on the file by running the command below before running SAW.
$ export HDF5_USE_FILE_LOCKING=FALSE
mapping
  • readNameSeparator error:
EXITING: FATAL INPUT ERROR: empty value for parameter “readNameSeparator” in input “Command-Line”
SOLUTION: use non-empty value for this parameter
Solution: try to delete --readNameSeparator \” \” from the command
  • limitBAMsortRAM error:
Error code: SAW-A10183

EXITING because of fatal ERROR: not enough memory for BAM sorting:
SOLUTION: re-run STAR with at least –limitBAMsortRAM xxxxxxxxx
Solution: Modify the value specified by the --limitBAMsortRAM refer to the SOLUTION in the stderr.
  • --limitOutSJcollapsed error:
EXITING because of fatal error: buffer size of SJ output is too small
Solution: increase input parameter --limitOutSJcollapsed
Solution: the parameters --limitOutSJcollapsed and --limitIObufferSize are paired. Please replace them with --limitOutSJcollapsed 10000000 --limitIObufferSize=480000000 and try again.
imageTools
  • OSError raises for imageTools merge
OSError: [Errno 30] Read-only file system: '/opt/saw_v5.4.0_software/pipeline/imageTools/imagetools-1.0.0/log'
Solution: Error raises because the -o input is a filename without path. Try to input /path/to/output/file.rpi or ./file.rpi for -o.
Appendix D: Error Codes
SAW error codes are designed to catch error information and describe it in an easily understood way. Users can use these messages to fix the problem by themselves. The error messages will be output to the "errcode.log" file.
The error code is designed to express in three parts, date-time, error code, and explanation. The date-time information could help users differentiate errors in different program executions. The error code part provides information for the pipeline modules and error types. The  explanation section displays the most explicit message stating the error/exception and possible solutions.
Pipeline
Code
Error type
Examples and error handling
splitMask
SAW-A00001
Parameters invalid or missing
e.g. "parameters error"Please check your input parameters.
Some required parameters might be missed.
e.g. "splitBcPos error, expected 1_24 or 2_25"
Please check your input CID position is either 1_24 or 2_25.
SAW-A00002
File open failed
Please check the input file exists and has the correct access permission.
SAW-A00003
File parse failed
e.g. "only support .bin or .h5 file."
Please check your input file is in the correct file format.
SAW-A00004
File open failed
e.g. "cannot write to file, /path/to/file"
Please check your output directory path is an existing path.
SAW-A00005
Other API error
Please check Appendix C or contact FAS/FBS for help.
SAW-A00006
Software exception
Please check Appendix C or contact FAS/FBS for help.
CIDCount
SAW-A00021
Parameters invalid or missing
Please check your input parameters. Some required parameters might be missed.
SAW-A00022
File open failed
e.g. "cannot open such file, /path/to/file"
Please check the input file exists and has the correct access permission.
SAW-A00023
Failed to parser the file
Please check your input file is in the correct file format.
SAW-A00024
Other API error
Please check Appendix C or contact FAS/FBS for help.
SAW-A00025
Software exception
Please check Appendix C or contact FAS/FBS for help.
mapping
SAW-A10101
Parameters invalid or missing
e.g. "EXITING: FATAL INPUT ERROR: unrecognized parameter name "outSAMattribute" in input "Command-Line-Initial""
Please check the spelling of your argument and parameters.
e.g. "please check the umi position and length"
Please check the length of the reads in FQ1 are consistent with the parameters set for barcode length and umi length. For example, the length of the sum of barcode and umi set in bcPara file is 35 bp, but one of the reads in FQ1 is 30 bp, then you will see A10101 error code. Please check the parameters set in the bcPara file are consistent with your FQs.
SAW-A10102
File open failed
e.g. "Error, cannot open the file which be expected in gz or ascii format"
Please check the file permission and file format.
e.g. "barcodePositionMapFile does not exists: /path/to/mask"
Please check the mask file exists and has the correct access permission.
SAW-A10103
File parse failed
e.g. "sequence and quality have different length"
Please check the completeness of the reads in FQ. This issue may arise if the FQs are in incorrect format or the file was incompletely written or transferred.
SAW-A10104
Invalid data or data exception
Error data. Please check the file format and content.
SAW-A10105
File deletion failed
This error arose if "_STARtmp" directory failed to be deleted. Please check whether the program has completely finished according to the *.Log.progress.out or *_barcodeMap.stat file.
SAW-A10106
File IO failed
Please contact FAS/FBS for help.
SAW-A10107
Failure on APIs of system and libraries
Please contact FAS/FBS for help.
SAW-A10108
Software assert
Please contact FAS/FBS for help.
SAW-A10109
Software exception
Please contact FAS/FBS for help.
SAW-A10110
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-A10111
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 FQs is not the same as the CID in the input mask file. Please use the correct SN-FQ pairs for mapping.
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.
count
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 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-A20009
Software exception
Please contact FAS/FBS for help.
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.
merge
SAW-A30001
Parameter missing
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/.bin mask file.
SAW-A30004
Fail to create output file
Fail to create output file. Please check your writing permission of the output directory.
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-A30006
Out of index
Record coordinates exceed the expected range. Please check the input file is the output of mapping.
SAW-A30007
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.
register & rapidRegister
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. Or, please check whether a stitched panoramic TIFF (.tif or .tiff) image exists in the TAR.GZ.
SAW-A40003
File parse failed
Please check your input file is in the correct file format. The -v input gene expression matrix should be either a *tsv, barcode_gene_exp.txt, *.gem.gz, or *raw.gef.
SAW-A40004
Invalid data or data exception
Error data. Please check the file content. This error may arise because the -v input file is empty, the CZI file in TAR.GZ is invalid, or the QCPassFlag in IPR is 0.
SAW-A40005
Tissue segmentation error
Abnormal tissue segmentation reference score in image preprocessing.
SAW-A40006
IPR field missing
"Stitch/BGIStitch/StitchedGlobalLoc", does not exist.
SAW-A40007
Tiled image missing
Please check the uncompressed image folder has tiled images.
imageTools
SAW-A40401
Parameter missing
Please check your imageTools merge input parameters. Some required parameters might be missed.
SAW-A40402
File open failed
Please check the imageTools merge input file that exists and has the correct access permission.
SAW-A40405
Invalid input
imageTools merge inputs of less than two images or more than three images.
SAW-A40406
File pairing failed
Please check the imageTools 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 imageTools overlay input parameters. Some required parameters might be missed.
SAW-A40502
File open failed
Please check the imageTools 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 -c input IPR file does not include Stitch/TransformTemplate or Register/MatrixTemplate information
SAW-A40601
Parameter missing
Please check your imageTools img2rpi input parameters. Some required parameters might be missed.
SAW-A40602
File open failed
Please check the imageTools img2rpi input file that exists and has the correct access permission.
SAW-A40605
Invalid input
imageTools img2rpi input -i and -g have different length. These two inputs are supposed to be paired.
SAW-A40701
Parameter missing
Please check your imageTools ipr2img input parameters. Some required parameters might be missed.
SAW-A40702
File open failed
Please check the imageTools ipr2imginput file exists and has the correct access permission. Or, please check whether a stitched panoramic TIFF (.tif or .tiff) image exists in the TAR.GZ.
SAW-A40703
File parse failed
Please check your imageTools ipr2img input file is in the imageQC/imageStudio output TAR.GZ format.
SAW-A40704
Invalid data or data exception
Error data. Please check the imageTools ipr2img input IPR file content.
This error may arise because the CZI file in TAR.GZ is invalid, or the image has not either automatically or manually registered with the expression matrix. The second circumstance can be confirmed from IPR by checking whether the StereoResepSwitch/register is TRUE (has not performed automatic registration) or the ManualState/register is FALSE (has not performed manual registration). The third possible reason is the StereoResepSwitch/tissueseg is TRUE, therefore cannot output cell segmentation result.
SAW-A40706
File pairing failed
Please check the shape of registered tissue segmentation images stored in the imageTools ipr2img input IPR are the same. Or please contact FAS/FBS for help.
tissueCut
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 H5 file attributes.
SAW-A50007
h5DatasetWrite error
Please check the H5 file dataset.
cellCut
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
e.g. "Please call freeRestriction first, or call restrictRegion function before restrictGene."
This error arose because the invocation flow order was messed up. Please modify your invocation flow as prompted.
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
Dimensions of gene expression matrix did not match
Please contact FAS/FBS for help.
spatialCluster
SAW-A70001
Parameter missing
e.g. "-i or --gef_file is missing"
Please check your input parameters. Some required parameters might be missed.
SAW-A70002
File open failed
e.g. “cannot access /path/to/file: No such file or directory.”
Please check the file that exists and has the correct access permission.
SAW-A70005
Value error
e.g. "The bin size is out of range, please check the range of gef binsize is in [1,10,20,50,100,200,500]."
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.
cellCluster
SAW-A70101
Parameter missing
e.g. "-i or --gef_file is missing"
Please check your input parameters. Some required parameters might be missed.
SAW-A70102
File open failed
e.g. “cannot access /path/to/file: No such file or directory.”
Please check the file that exists and has the correct access permission.
SAW-A70105
Value error
e.g. "The bin size is out of range, please check the range of gef binsize is in [1,10,20,50,100,200,500]."
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.
saturation
SAW-A80001
Parameter missing
e.g. "-i is 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
File parse failed
Invalid GEF file. Please check the file format.
SAW-A80004
Invalid data or data exception
e.g. "no data left after filter by coordinates."
Please check the file content.
SAW-A80005
Invalid data or data exception
e.g. "total map reads is 0, please check file format from --bcstat"
Please check the file content of the input file as prompted.
SAW-A80006
File pairing failed
e.g. "map reads less than annotated reads."
Please check the input mapping statistical report and the count statistical report are from the same analysis.
SAW-A80007
Plot error
Please contact FAS/FBS for help. PATH environment may not have python3.
SAW-A80008
Fail to create output file
Fail to generate saturation file, please contact FAS/FBS for help.
report
SAW-A90001
Parameter missing
e.g. "-m or --barcodeMapStat is missing."
Please check your input parameter as prompted. Some required parameters might be missed.
SAW-A90002
File open failed
e.g. "cannot access *: No such file or directory."
Please check the file that exists and has the correct access permission.
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 as report. Or, the input mapping file prefix can not be parsed. Please contact FAS/FBS for help.
SAW-A90004
Invalid data or data exception
e.g."information loss: fail to find 'bin_[size]' or 'ssDNA' in '*.rpi'."
Please check the file content.
SAW-A90005
Fail to create output file
Fail to create output file. Please check your writing permission of the output directory.
manualRegister
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. Or, please check whether the pre-registered image fov_stitched_transformed.tif exists in the input directory.
SAW-A40803
File parse failed
Please check your input file is in the correct file format. The -v input gene expression matrix should be either a *tsv, barcode_gene_exp.txt, *.gem.gz, or *raw.gef.
SAW-A40804
Invalid data or data exception
Error data. Please check the file content. This error may arise because the -v input file is empty. The second possible reason is that the gene expression matrix information in the IPR 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.
References
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