ciccalab / simpli Goto Github PK
View Code? Open in Web Editor NEWSIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
Home Page: https://github.com/ciccalab/SIMPLI/wiki
License: Other
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
Home Page: https://github.com/ciccalab/SIMPLI/wiki
License: Other
Hey Michele,
I'm trying to run SIMPLI again but I'm getting an issue at the clustering step. This is the clustering_log.txt output:
Loading required package: ggplot2
Loading required package: cowplot
Loading required package: Matrix
Registered S3 method overwritten by 'gplots':
method from
reorder.factor gdata
Warning: namespace ‘dimRed’ is not available and has been replaced
by .GlobalEnv when processing object ‘<unknown>’
Warning: namespace ‘dimRed’ is not available and has been replaced
by .GlobalEnv when processing object ‘<unknown>’
[1] "annotated_cells.csv"
[2] "sample_metadata_SEN.csv"
[3] "all_cells"
[4] "Intensity_MeanIntensity_CD163@Intensity_MeanIntensity_p16@Intensity_MeanIntensity_yH2AX@Intensity_MeanIntensity_OLIG2@Intensity_MeanIntensity_p21@Intensity_MeanIntensity_MAP2@Intensity_MeanIntensity_GLB1@Intensity_MeanIntensity_GFAP@Intensity_MeanIntensity_Ki67@Intensity_MeanIntensity_Iba1@Intensity_MeanIntensity_GLUT1"
[5] "0.4"
[6] "all_cells"
[7] "all_cells"
Reading the clustering data by sample
Scaling and centering clustering data by sample.
Error in (function (cl, name, valueClass) :
assignment of an object of class “NULL” is not valid for @‘cell.names’ in an object of class “seurat”; is(value, "vector") is not TRUE
Calls: lapply -> FUN -> CreateSeuratObject -> <Anonymous>
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
I've run your code from Seurat_Runner.R up to creating the seurats_by_sample
object on my RStudio and it works, but I have the new version of Seurat. Do you have any suggestions on how to fix it?
Thanks a lot for your help!
Lines 1 to 3 in 09e3bd4
Apptainer is the successor of Singularity.
$ curl https://singularity.hpcng.org/
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="refresh" content="0; url='https://apptainer.org/index.html'" />
</head>
<body>
<h2 style="text-align: center; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif;">This page has been moved to our new domain! ( apptainer.org ). Please wait well we redirect you. </h2>
[…]
Nextflow supports a variety of container runtimes, including Apptainer. It’d be nice, if SIMPLI would support it too and not hardcode Singularity.
$ ./launch.sh run https://github.com/ciccalab/SIMPLI -profile test -with-apptainer /dev/shm/nextflow/singularity/containers/simpli_imaging-default-simpli_imctools_stardist-test.img
N E X T F L O W ~ version 23.02.1-edge
Launching `https://github.com/ciccalab/SIMPLI` [condescending_dalembert] DSL2 - revision: 09e3bd432a [master]
Cannot enable more than one container engine -- Choose either one of: singularity, apptainer
Running SIMPLI’s test profile fails with the error below in our environment:
$ javac -version
javac 17.0.2-internal
$ singularity version
3.8.3+231-g9dceb4240
$ git log --oneline --no-decorate -1
7236f830a Fix Orphaned processes when using Singularity
$ ./launch.sh -v
nextflow version 23.02.1-edge.5846
$ ./launch.sh run https://github.com/ciccalab/SIMPLI -profile test
N E X T F L O W ~ version 23.02.1-edge
Launching `https://github.com/ciccalab/SIMPLI` [high_mcnulty] DSL2 - revision: 09e3bd432a [master]
executor > local (2)
[37/ac837e] process > convert_raw_data:convert_raw_data_to_tiffs (2) [ 0%] 0 of 2
[- ] process > convert_raw_data:collect_raw_tiff_metadata -
[- ] process > normalize_images:normalize_tiffs -
[- ] process > normalize_images:collect_normalized_tiff_metadata -
[- ] process > preprocess_images:image_preprocessing -
[- ] process > preprocess_images:process_preprocessed_metadata -
[- ] process > measure_areas:measure_positive_areas -
[- ] process > cp_segment_cells:cp_cell_segmentation -
[- ] process > cp_segment_cells:collect_single_cell_data -
[- ] process > sd_segment_cells:sd_cell_segmentation -
[- ] process > sd_segment_cells:collect_single_cell_data -
[- ] process > identify_cell_types_mask:cell_type_identification_mask -
[- ] process > threshold_expression:threshold_cells -
[- ] process > cluster_cells:cell_clustering -
[- ] process > cluster_cells:collect_clustering_data -
[- ] process > analyse_homotypic_interactions:homotypic_interaction_analysis -
[- ] process > analyse_homotypic_interactions:collect_homotypic_interactions -
[- ] process > calculate_heterotypic_distances:get_heterotypic_distances -
[- ] process > calculate_heterotypic_distances:collect_heterotypic_distances -
[- ] process > permute_heterotypic_interactions:permute_heterotypic_distances -
[- ] process > visualize_areas:area_visualization -
[- ] process > visualize_cell_types:cell_type_visualization -
[- ] process > visualize_cell_clusters:cell_cluster_visualization -
[- ] process > visualize_cell_thresholds:cell_threshold_visualization -
[- ] process > visualize_homotypic_interactions:homotypic_interaction_visualization -
[- ] process > visualize_heterotypic_interactions:heterotypic_interaction_visualization -
[- ] process > visualize_permuted_interactions:permuted_interaction_visualization -
Error executing process > 'convert_raw_data:convert_raw_data_to_tiffs (2)'
Caused by:
Process `convert_raw_data:convert_raw_data_to_tiffs (2)` terminated with an error exit status (1)
Command executed:
python3.8 /opt/Tiff_extracter.py \
CRC_2 \
'ROI004_R-A02_x13400_800-y12700_1250-p0014-200Hz-p07dB-s0137' \
executor > local (2)
[cc/e822d9] process > convert_raw_data:convert_raw_data_to_tiffs (1) [100%] 1 of 1, failed: 1
[- ] process > convert_raw_data:collect_raw_tiff_metadata -
[- ] process > normalize_images:normalize_tiffs -
[- ] process > normalize_images:collect_normalized_tiff_metadata -
[- ] process > preprocess_images:image_preprocessing -
[- ] process > preprocess_images:process_preprocessed_metadata -
[- ] process > measure_areas:measure_positive_areas -
[- ] process > cp_segment_cells:cp_cell_segmentation -
[- ] process > cp_segment_cells:collect_single_cell_data -
[- ] process > sd_segment_cells:sd_cell_segmentation -
[- ] process > sd_segment_cells:collect_single_cell_data -
[- ] process > identify_cell_types_mask:cell_type_identification_mask -
[- ] process > threshold_expression:threshold_cells -
[- ] process > cluster_cells:cell_clustering -
[- ] process > cluster_cells:collect_clustering_data -
[- ] process > analyse_homotypic_interactions:homotypic_interaction_analysis -
[- ] process > analyse_homotypic_interactions:collect_homotypic_interactions -
[- ] process > calculate_heterotypic_distances:get_heterotypic_distances -
[- ] process > calculate_heterotypic_distances:collect_heterotypic_distances -
[- ] process > permute_heterotypic_interactions:permute_heterotypic_distances -
[- ] process > visualize_areas:area_visualization -
[- ] process > visualize_cell_types:cell_type_visualization -
[- ] process > visualize_cell_clusters:cell_cluster_visualization -
[- ] process > visualize_cell_thresholds:cell_threshold_visualization -
[- ] process > visualize_homotypic_interactions:homotypic_interaction_visualization -
[- ] process > visualize_heterotypic_interactions:heterotypic_interaction_visualization -
[- ] process > visualize_permuted_interactions:permuted_interaction_visualization -
Error executing process > 'convert_raw_data:convert_raw_data_to_tiffs (2)'
Caused by:
Process `convert_raw_data:convert_raw_data_to_tiffs (2)` terminated with an error exit status (1)
Command executed:
python3.8 /opt/Tiff_extracter.py \
CRC_2 \
'ROI004_R-A02_x13400_800-y12700_1250-p0014-200Hz-p07dB-s0137' \
crc_2.txt \
single \
./ \
channel_metadata.csv \
CRC_2-raw_tiff_metadata.csv > extract_log.txt 2>&1
Command exit status:
1
Command output:
(empty)
Command error:
INFO: Converting SIF file to temporary sandbox...
WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts
INFO: Cleaning up image...
Work dir:
/dev/shm/nextflow/work/37/ac837e73cad46da68cc57e2a64ec93
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
No idea, if the Singularity warning is a red herring, and something else causes this.
Is there a way to run that single Singularity “step” directly?
Hi Michele,
can you please make the Singularity image available?
Thanks,
Alessia
Hi!
I have a problem running SIMPLI with multiple single channel samples. The problem is that SIMPLI normalizes only the first sample from the sample_metadata file. To better understand the problem I printed some output from the Nextflow process. It seems that the main.nf and workflow.nf reads the samples correct, but only the sample_1 is passed to the process.nf and that is why the sample_2 is not normalized. If I run the pipeline with SIMPLI test data everything works fine. With my data I skip the extraction step because I'm using single channel tiff images.
My terminal output:
N E X T F L O W ~ version 21.10.6
Launching main.nf
[backstabbing_celsius] - revision: 1548360ea3
executor > local (2)
[b9/f24b98] process > normalize_images:normalize_tiffs (1) [100%] 1 of 1 ✔
[14/107818] process > normalize_images:collect_normalize... [100%] 1 of 1 ✔
sample (printed from: main.nf) : sample_1
sample (printed from: workflow normalize_images) : sample_1
sample (printed from: main.nf) : sample_2
sample (printed from: workflow normalize_images) : sample_2
sample (printed from: process normalize_tiffs): sample_1
My metadata files are attached:
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