# Run failed with .csv.gz input file, access denied to output log **URL:** \ **Category:** MapMyCells\ **Tags:** atlas-cell-types, analysis\ **Created:** [February 18, 2026, 4:30pm UTC](https://community.brain-map.org/t/run-failed-with-csv-gz-input-file-access-denied-to-output-log/4853 "2026-02-18T16:30:26Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![ddressman91](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/ddressman91/32/2530_2.png) [@ddressman91](https://community.brain-map.org/u/ddressman91)\ **Post date:** [February 18, 2026, 4:30pm UTC](https://community.brain-map.org/t/run-failed-with-csv-gz-input-file-access-denied-to-output-log/4853/1 "2026-02-18T16:30:26Z")
I recently submitted a .csv.gz input file, with cells as rows and genes as columns, to MapMyCells. The run failed (run ID 1771365448267-9bf9ae75-bafb-475c-8529-785359b31b74), and when I tried to download the logs, it opened a new tab with this message (after I disabled my popup blocker): “This XML file does not appear to have any style information associated with it. The document tree is shown below. `AccessDenied` Access Denied ” I copied a snippet of the count matrix .csv file below, from before I gzipped it (it is now .csv.gz). I tried re-running it, as this worked for another user, but this also failed and I got the same access denied message on the logs (run ID 1771365448267-9bf9ae75-bafb-475c-8529-785359b31b74 for the second try). ```auto MIR1302-2HG FAM138A OR4F5 AL627309.1 AL627309.3 ``` EZ087\_seurat\_AAACAGCCATAGCGAG.1 0 0 0 0 0 EZ087\_seurat\_AAACATGCAAGTGTCC.1 0 0 0 0 0 EZ087\_seurat\_AAACATGCAATAATGG.1 0 0 0 1 0 EZ087\_seurat\_AAACATGCAATGAATG.1 0 0 0 0 0 EZ087\_seurat\_AAACATGCACCTGCTC.1 0 0 0 0 0 EZ087\_seurat\_AAACCAACAAACCTTG.1 0 0 0 0 0 AL627309.4 EZ087\_seurat\_AAACAGCCATAGCGAG.1 0 EZ087\_seurat\_AAACATGCAAGTGTCC.1 0 EZ087\_seurat\_AAACATGCAATAATGG.1 0 EZ087\_seurat\_AAACATGCAATGAATG.1 0 EZ087\_seurat\_AAACATGCACCTGCTC.1 0 EZ087\_seurat\_AAACCAACAAACCTTG.1 0 It’s possible that my .csv.gz file has quotation marks for the column giving the cell names, but a previous post led me to understand that MapMyCells would be configured to allow this. ---
**Author:** ![ddressman91](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/ddressman91/32/2530_2.png) [@ddressman91](https://community.brain-map.org/u/ddressman91)\ **Post date:** [February 18, 2026, 4:31pm UTC](https://community.brain-map.org/t/run-failed-with-csv-gz-input-file-access-denied-to-output-log/4853/2 "2026-02-18T16:31:33Z")
For some reason the first five column names of the .csv file snipped copied in as code, but they should be text. ---
**Author:** ![danielsf](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/danielsf/32/209_2.png) [@danielsf](https://community.brain-map.org/u/danielsf)\ **Post date:** [February 18, 2026, 5:42pm UTC](https://community.brain-map.org/t/run-failed-with-csv-gz-input-file-access-denied-to-output-log/4853/3 "2026-02-18T17:42:37Z")
Hi @ddressman91 I acknowledge that the answer I’m about to give you is not very satisfactory. Failing and then not allowing you to download the logs is generally a sign that the cloud instance running MapMyCells ran out of memory. Crashing because of an “out of memory” error does not give the machine a chance to write any output for download. Something about your data (~131,000 cells by ~27,000 genes) provoked such a crash. Memory use in MapMyCells is a bit complicated. It is governed by the number of processors assigned to a job, the number of cells each processor is told to map at a time, and the number of marker genes in the taxonomy (this is probably what got you; the Whole Human Brain taxonomy involves more marker genes than Whole Mouse Brain). Anyway: I downloaded your data, grabbed the first 50,000 cells, wrote them to a CSV file, gzipped it, and was able to successfully map them. I would recommend that you just split up your data into slightly smaller chunks and map each chunk individually (again: 50,000 cells seems fine). We probably need to do some work on MapMyCells so that it manages memory a little better (dynamically setting the number of cells processed by each processor based on how many genes are in the data). That will take some time. In the meantime: smaller sized inputs are your friend. I hope that gets you unblocked. Cheers, Scott ---
**Author:** ![ddressman91](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/ddressman91/32/2530_2.png) [@ddressman91](https://community.brain-map.org/u/ddressman91)\ **Post date:** [February 18, 2026, 7:04pm UTC](https://community.brain-map.org/t/run-failed-with-csv-gz-input-file-access-denied-to-output-log/4853/4 "2026-02-18T19:04:52Z")
That’s fine, thanks for the info. I was going by the Gb limit for input files, but previous to making my full gzipped file, I split the count matrix into 4 parts, so I will probably submit those individually and try again. ---
**Author:** ![ddressman91](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/ddressman91/32/2530_2.png) [@ddressman91](https://community.brain-map.org/u/ddressman91)\ **Post date:** [February 18, 2026, 9:34pm UTC](https://community.brain-map.org/t/run-failed-with-csv-gz-input-file-access-denied-to-output-log/4853/5 "2026-02-18T21:34:07Z")
Hi Scott, Chunks 1-3 ran fine, but I got an error on chunk 4. I pasted the text of the validation log below if you can’t see it, run ID is 1771449255044-12064d00-2ec9-4c2d-a3f7-0ceb6ad26034. It looks like there’s an NA somewhere (or several of them) that is causing the problem, but I checked the cell names and the count matrix in R and couldn’t find any NA’s. Could NA’s be introduced in the conversion to an .h5ad file or conversion between gene symbols and ENSEMBL IDs? Log text: 5.10693e-04 seconds == WARNING: Input data is in CSV format; converting to h5ad file at MSA.ctrl.PD.snRNAseq.countmatrix.slice4.csv-2026-02-18-21-19-51.h5ad 7.94722e+01 seconds == an ERROR occurred ==== Traceback (most recent call last): File cell\_type\_mapper/validation/csv\_utils.py, line 99, in convert\_csv\_to\_h5ad adata = anndata.io.read\_csv( File anndata/\_io/read.py, line 49, in read\_csv return read\_text(filename, delimiter, first\_column\_names, dtype) File anndata/\_io/read.py, line 351, in read\_text return \_read\_text(f, delimiter, first\_column\_names, dtype) File anndata/\_io/read.py, line 440, in \_read\_text data.append(np.array(line\_list[1:], dtype=dtype)) ValueError: could not convert string to float: ‘NA’ During handling of the above exception, another exception occurred: Traceback (most recent call last): File cell\_type\_mapper/cli/validate\_h5ad.py, line 242, in run result\_path, has\_warnings = validate\_h5ad( File cell\_type\_mapper/validation/validate\_h5ad.py, line 97, in validate\_h5ad result = \_validate\_h5ad( File cell\_type\_mapper/validation/validate\_h5ad.py, line 136, in \_validate\_h5ad write\_to\_new\_path) = convert\_csv\_to\_h5ad( File cell\_type\_mapper/validation/csv\_utils.py, line 110, in convert\_csv\_to\_h5ad raise RuntimeError(full\_msg) RuntimeError: =======An error occurred when reading your CSV with anndata: Traceback (most recent call last): File cell\_type\_mapper/validation/csv\_utils.py, line 99, in convert\_csv\_to\_h5ad adata = anndata.io.read\_csv( File anndata/\_io/read.py, line 49, in read\_csv return read\_text(filename, delimiter, first\_column\_names, dtype) File anndata/\_io/read.py, line 351, in read\_text return \_read\_text(f, delimiter, first\_column\_names, dtype) File anndata/\_io/read.py, line 440, in \_read\_text data.append(np.array(line\_list[1:], dtype=dtype)) ValueError: could not convert string to float: ‘NA’ Please confirm that your CSV is a table in which each row is a cell and each column is a gene. 7.94722e+01 seconds == CLEANING UP 7.95488e+01 seconds == Mapping algorithm failed because of application errors. 7.95488e+01 seconds == Validation error: e=RuntimeError(‘=======An error occurred when reading your CSV with anndata:\nTraceback (most recent call last):\n File “/usr/local/lib/python3.10/site-packages/cell\_type\_mapper/validation/csv\_utils.py”, line 99, in convert\_csv\_to\_h5ad\n adata = anndata.io.read\_csv(\n File “/usr/local/lib/python3.10/site-packages/anndata/\_io/read.py”, line 49, in read\_csv\n return read\_text(filename, delimiter, first\_column\_names, dtype)\n File “/usr/local/lib/python3.10/site-packages/anndata/\_io/read.py”, line 351, in read\_text\n return \_read\_text(f, delimiter, first\_column\_names, dtype)\n File “/usr/local/lib/python3.10/site-packages/anndata/\_io/read.py”, line 440, in \_read\_text\n data.append(np.array(line\_list[1:], dtype=dtype))\nValueError: could not convert string to float: ‘NA’\n\nPlease confirm that your CSV is a table in which each row is a cell and each column is a gene.’), type(e)=\, fname=‘run.py’, lineno=153 Traceback (most recent call last): File “/usr/local/lib/python3.10/site-packages/cell\_type\_mapper/validation/csv\_utils.py”, line 99, in convert\_csv\_to\_h5ad adata = anndata.io.read\_csv( File “/usr/local/lib/python3.10/site-packages/anndata/\_io/read.py”, line 49, in read\_csv return read\_text(filename, delimiter, first\_column\_names, dtype) File “/usr/local/lib/python3.10/site-packages/anndata/\_io/read.py”, line 351, in read\_text return \_read\_text(f, delimiter, first\_column\_names, dtype) File “/usr/local/lib/python3.10/site-packages/anndata/\_io/read.py”, line 440, in \_read\_text data.append(np.array(line\_list[1:], dtype=dtype)) ValueError: could not convert string to float: ‘NA’ During handling of the above exception, another exception occurred: Traceback (most recent call last): File “/apps/run.py”, line 153, in run runner.run() File “/usr/local/lib/python3.10/site-packages/cell\_type\_mapper/cli/validate\_h5ad.py”, line 242, in run result\_path, has\_warnings = validate\_h5ad( File “/usr/local/lib/python3.10/site-packages/cell\_type\_mapper/validation/validate\_h5ad.py”, line 97, in validate\_h5ad result = \_validate\_h5ad( File “/usr/local/lib/python3.10/site-packages/cell\_type\_mapper/validation/validate\_h5ad.py”, line 136, in \_validate\_h5ad write\_to\_new\_path) = convert\_csv\_to\_h5ad( File “/usr/local/lib/python3.10/site-packages/cell\_type\_mapper/validation/csv\_utils.py”, line 110, in convert\_csv\_to\_h5ad raise RuntimeError(full\_msg) RuntimeError: =======An error occurred when reading your CSV with anndata: Traceback (most recent call last): File “/usr/local/lib/python3.10/site-packages/cell\_type\_mapper/validation/csv\_utils.py”, line 99, in convert\_csv\_to\_h5ad adata = anndata.io.read\_csv( File “/usr/local/lib/python3.10/site-packages/anndata/\_io/read.py”, line 49, in read\_csv return read\_text(filename, delimiter, first\_column\_names, dtype) File “/usr/local/lib/python3.10/site-packages/anndata/\_io/read.py”, line 351, in read\_text return \_read\_text(f, delimiter, first\_column\_names, dtype) File “/usr/local/lib/python3.10/site-packages/anndata/\_io/read.py”, line 440, in \_read\_text data.append(np.array(line\_list[1:], dtype=dtype)) ValueError: could not convert string to float: ‘NA’ Please confirm that your CSV is a table in which each row is a cell and each column is a gene. ---
**Author:** ![danielsf](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/danielsf/32/209_2.png) [@danielsf](https://community.brain-map.org/u/danielsf)\ **Post date:** [February 18, 2026, 9:42pm UTC](https://community.brain-map.org/t/run-failed-with-csv-gz-input-file-access-denied-to-output-log/4853/6 "2026-02-18T21:42:35Z")
Hi, I downloaded your slice4.csv.gz file. For some reason, the last line of your CSV is entirely made up of `NA` (even the cell label is `"NA”`). I wonder if R “just knows” to skip that line, which is why it didn’t turn up in your debugging efforts. Anyway: clip that line off and you should be fine. Cheers, Scott