cellranger and velocyto runs

Author: craniolab

.gitignore

@@ -5,3 +5,4 @@ cellranger_related/cellranger_output/
 cellranger_related/cellranger-9.0.1/
 cellranger_related/cellranger-atac-2.1.0/
 sequencing_results/
+h5ad_files/

cellranger_related/cellranger_code/cellranger_count/job.8681691.err

@@ -0,0 +1,20 @@
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names

cellranger_related/cellranger_code/cellranger_count/job.8681691.out

@@ -0,0 +1,15 @@
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.

cellranger_related/cellranger_code/cellranger_count/job.8681692.err

@@ -0,0 +1,19 @@
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names

cellranger_related/cellranger_code/cellranger_count/job.8681692.out

@@ -0,0 +1,15 @@
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.

cellranger_related/cellranger_code/cellranger_count/job.8681703.err

@@ -0,0 +1,36 @@
+
+
+Could not find a 10x cloud token in the default user directory.  In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
+tar: Removing leading `/' from member names
+error: Found argument '--output-dir' which wasn't expected, or isn't valid in this context
+
+	If you tried to supply `--output-dir` as a value rather than a flag, use `-- --output-dir`
+
+USAGE:
+    cellranger count --id <ID> --transcriptome <PATH>
+
+For more information try --help
+error: Found argument '--output-dir' which wasn't expected, or isn't valid in this context
+
+	If you tried to supply `--output-dir` as a value rather than a flag, use `-- --output-dir`
+
+USAGE:
+    cellranger count --id <ID> --transcriptome <PATH>
+
+For more information try --help
+error: Found argument '--output-dir' which wasn't expected, or isn't valid in this context
+
+	If you tried to supply `--output-dir` as a value rather than a flag, use `-- --output-dir`
+
+USAGE:
+    cellranger count --id <ID> --transcriptome <PATH>
+
+For more information try --help
+error: Found argument '--output-dir' which wasn't expected, or isn't valid in this context
+
+	If you tried to supply `--output-dir` as a value rather than a flag, use `-- --output-dir`
+
+USAGE:
+    cellranger count --id <ID> --transcriptome <PATH>
+
+For more information try --help