# Could not extract FINN emission file in CMAQv5.4 **URL:** \ **Category:** CMAQ\ **Created:** [October 15, 2024, 9:39am UTC](https://forum.cmascenter.org/t/could-not-extract-finn-emission-file-in-cmaqv5-4/5285 "2024-10-15T09:39:52Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![Starry](https://avatars.discourse-cdn.com/v4/letter/s/2bfe46/32.png) [@Starry](https://forum.cmascenter.org/u/Starry)\ **Post date:** [October 15, 2024, 9:39am UTC](https://forum.cmascenter.org/t/could-not-extract-finn-emission-file-in-cmaqv5-4/5285/1 "2024-10-15T09:39:52Z")
Dear All I use [finn2cmaq](https://github.com/barronh/finn2cmaq) to output FINN emission and add it to CMAQv5.4 (with cb6r3\_ae7 mechanism) but get an error. ![30d88d4afb7fb3f4539d7db85ab1396](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/2X/f/fd3a09da00d929b906053dd5327143d17937852f.png) ![94538e656e95847e1ea7b0c578a5e1d](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/2X/a/af7561592fca2859f43788770f8530b0e88ee126.png) I check [this post](https://forum.cmascenter.org/t/could-not-extract-gr-emis-001-file-in-cmaq-run/1497/10) and add the missing species (the value is 0) with gspro of finn2cmaq but get the same error. Here is my log [CTM\_LOG\_001.v54\_intel\_tibet27km\_20220727.txt](https://forum.cmascenter.org/uploads/short-url/voEuo7RdVHBAlPAZByLQPUV4wnV.txt) (22.1 KB) the [FINN emission file](https://drive.google.com/file/d/1vjH3MFd79ICkVTTh6arQHzoBMfrTLWEp/view?usp=sharing) the CMAQ\_Control\_DESID\_cb6r3\_ae7\_aq.nml file [CMAQ\_Control\_DESID\_cb6r3\_ae7\_aq.nml.txt](https://forum.cmascenter.org/uploads/short-url/tzfbQK5mEhby4rrHEYSnjunxXY8.txt) (14.8 KB) the gspro of finn2cmaq [gc12\_to\_cb6r3\_ae7\_v2.txt](https://forum.cmascenter.org/uploads/short-url/w70QrRwuxrwaUYOdeMrGRHUCRCi.txt) (3.1 KB) Any advice would be appreciated. Li ---
**Author:** ![barronh](https://avatars.discourse-cdn.com/v4/letter/b/85e7bf/32.png) [@barronh](https://forum.cmascenter.org/u/barronh)\ **Post date:** [October 15, 2024, 2:55pm UTC](https://forum.cmascenter.org/t/could-not-extract-finn-emission-file-in-cmaqv5-4/5285/2 "2024-10-15T14:55:41Z")
You say “the missing species.” Which species is missing? I don’t see a species name in the log. ---
**Author:** ![Starry](https://avatars.discourse-cdn.com/v4/letter/s/2bfe46/32.png) [@Starry](https://forum.cmascenter.org/u/Starry)\ **Post date:** [October 16, 2024, 5:23am UTC](https://forum.cmascenter.org/t/could-not-extract-finn-emission-file-in-cmaqv5-4/5285/3 "2024-10-16T05:23:50Z")
Hi barronh Thank you very much for your reply. I compared the var-list between the output of finn2cmaq and SMOKE which ran successfully and found these species are missing: ALDX, ISOP, MEOH, NVOL, OLE, PH2O, SULF, TERP, UNK, UNR, VOC\_INC, XYL. ![b3b4b6aad55dd6eb28b23939a20e3e5](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/2X/0/0aed8f9896521e39977ac4be68888c0d4d34edb1.png) However, I found the number of species in my emission file of MEGANv2.1 is 25. I also marked the species that were missing from the output of finn2cmaq: ISOP, TERP, XYL, OLE, NR, MEOH, CH4, ETOH, ALDX. ![c979eb207d00fa85109a05381e8f182](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/2X/4/442a6367260fd1330dc58189990ac168bcdc7f00.png) The same missing species are ALDX, ISOP, MEOH, OLE, TERP, XYL. I don’t know if the error was caused by missing these species or if there were other causes. And also I didn’t use the original txt2daily.py scripts I changed it to use FINNv2.5 data. Could this cause the problem? ![1729056777532](https://canada1.discourse-cdn.com/flex027/uploads/cmas/original/2X/b/b23fb1fe1b6e5577ea145451565cd64d885117e0.png) Thanks a lot. Li ---
**Author:** ![hogrefe.christian](https://avatars.discourse-cdn.com/v4/letter/h/74df32/32.png) [@hogrefe.christian](https://forum.cmascenter.org/u/hogrefe.christian)\ **Post date:** [October 16, 2024, 9:41pm UTC](https://forum.cmascenter.org/t/could-not-extract-finn-emission-file-in-cmaqv5-4/5285/4 "2024-10-16T21:41:35Z")
I am not familiar with @barronh 's finn2cmaq tool, but it might help if you could post a text file containing the output of `ncdump -h /public5/home/sch6618/soft/model/CMAQv5.4/data/emis/tibet27km/FINNv2.5_2022.GEOSCHEM.nc` . Something in the structure or content of this file causes CMAQ’s read function to fail. ---
**Author:** ![Starry](https://avatars.discourse-cdn.com/v4/letter/s/2bfe46/32.png) [@Starry](https://forum.cmascenter.org/u/Starry)\ **Post date:** [October 17, 2024, 1:23am UTC](https://forum.cmascenter.org/t/could-not-extract-finn-emission-file-in-cmaqv5-4/5285/5 "2024-10-17T01:23:47Z")
Hi hogrefe.christian Thank you very much for your reply. Here is the txt file. [FINN.txt](https://forum.cmascenter.org/uploads/short-url/tQKTTdqvamyEvXMspjVEq1G0HFc.txt) (27.1 KB) ---
**Author:** ![hogrefe.christian](https://avatars.discourse-cdn.com/v4/letter/h/74df32/32.png) [@hogrefe.christian](https://forum.cmascenter.org/u/hogrefe.christian)\ **Post date:** [October 17, 2024, 6:47am UTC](https://forum.cmascenter.org/t/could-not-extract-finn-emission-file-in-cmaqv5-4/5285/6 "2024-10-17T06:47:23Z")
Thanks for posting the full header of your file. Overall, nothing really inconsistent stood out to me, but I did notice that the HISTORY attribute shows that `ncrcat` was used to string together about 40 individual day-specific FINN files into this final file with 975 hourly time steps. Was this done as part of running finn2cmaq, or afterwards? Generally, using NCO or CDO operators on files conforming to I/O API conventions will generate output files that violate these conventions and cannot be used as input to CMAQ or other tools that use the I/O API library for file input. In particular, using such operators will often mess up TFLAG which then renders the file not usable by I/O API functions. A simple test to see if file `FINNv2.5_2022.GEOSCHEM.nc` conforms to conventions is to use it as input to `m3stat` or other ‘m3tools’ programs. If this fails, it will also fail when used as input to CMAQ. If using `ncrcat` outside of `finn2cmaq` was indeed the problem while the original day-specific files generated by `finn2cmaq` were fine, you could instead use ‘m3tools’ like `m3xtract` to concatenate these files into the longer time period for which you want to create your FINN emissions file. ---
**Author:** ![Starry](https://avatars.discourse-cdn.com/v4/letter/s/2bfe46/32.png) [@Starry](https://forum.cmascenter.org/u/Starry)\ **Post date:** [October 17, 2024, 9:25am UTC](https://forum.cmascenter.org/t/could-not-extract-finn-emission-file-in-cmaqv5-4/5285/7 "2024-10-17T09:25:49Z")
Hi hogrefe.christian Thank you very much. Yes, I use ncrcat outside of finn2cmaq to combine multiple days as one. And this causes the error. I used m3cple instead and it finally worked successfully. Thanks again, It helps me a lot. ---
**Author:** ![cjcoats](https://avatars.discourse-cdn.com/v4/letter/c/ac8455/32.png) [@cjcoats](https://forum.cmascenter.org/u/cjcoats)\ **Post date:** [October 17, 2024, 12:22pm UTC](https://forum.cmascenter.org/t/could-not-extract-finn-emission-file-in-cmaqv5-4/5285/8 "2024-10-17T12:22:35Z")
This is not a correctly formed I/O API file. In particular, it is missing **many** of the required header-attributes, including particularly `VAR-LIST` (and also `SDATE, STIME, TSTEP, NCOLS, NROWS, NTHIK, NVARS, GDTYP, P_ALP, P_BET, p_GAM, XCENT, YCENT, XCELL, YCELL, XORIG, YORIG`) ---
**Author:** ![Starry](https://avatars.discourse-cdn.com/v4/letter/s/2bfe46/32.png) [@Starry](https://forum.cmascenter.org/u/Starry)\ **Post date:** [October 17, 2024, 12:42pm UTC](https://forum.cmascenter.org/t/could-not-extract-finn-emission-file-in-cmaqv5-4/5285/9 "2024-10-17T12:42:54Z")
Hi cjcoats Thank you very much for your reply. I will remember this.