# Java Error Message when writing output in hail **URL:** \ **Category:** Hail Query & hailctl\ **Created:** [December 2, 2021, 8:26pm UTC](https://discuss.hail.is/t/java-error-message-when-writing-output-in-hail/2391 "2021-12-02T20:26:28Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![sph17](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/sph17/32/684_2.png) [@sph17](https://discuss.hail.is/u/sph17)\ **Post date:** [December 2, 2021, 8:26pm UTC](https://discuss.hail.is/t/java-error-message-when-writing-output-in-hail/2391/1 "2021-12-02T20:26:28Z")
I am trying to run a vcf filtering script with hail via Terra’s virtual environment. The configuration is attached. ![Screen Shot 2021-11-30 at 1.51.30 PM](https://canada1.discourse-cdn.com/flex036/uploads/hail/original/1X/8b7b3c9721b9059a4bad7e4b875d20241c4db1c4.png) The python script that calls hail had no problem running but at the last step of writing to the output vcf location, hail throws a java error. Any suggestions would be greatly appreciated. The stdout log below: [hail\_1202\_stdout.txt](https://discuss.hail.is/uploads/short-url/iK9i1Dco7rwgr38H8sNihoZyMlY.txt) (6.4 KB) ---
**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\ **Post date:** [December 2, 2021, 8:27pm UTC](https://discuss.hail.is/t/java-error-message-when-writing-output-in-hail/2391/2 "2021-12-02T20:27:54Z")
Can you post the script? ---
**Author:** ![sph17](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/sph17/32/684_2.png) [@sph17](https://discuss.hail.is/u/sph17)\ **Post date:** [December 3, 2021, 3:15pm UTC](https://discuss.hail.is/t/java-error-message-when-writing-output-in-hail/2391/3 "2021-12-03T15:15:20Z")
Here is the script I’m trying to run: > **[wgs\_pre\_processing\_vcf\_v3\_Loose\_Filters.py](https://www.dropbox.com/s/g36gyokmvbxlf4h/wgs_pre_processing_vcf_v3_Loose_Filters.py?dl=0)** > > Shared with Dropbox ---
**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\ **Post date:** [December 3, 2021, 3:18pm UTC](https://discuss.hail.is/t/java-error-message-when-writing-output-in-hail/2391/4 "2021-12-03T15:18:53Z")
How big is the VCF? This looks like it’s probably a memory error – you’re running on a pretty tiny VM. You could try increasing the size of the machine provisioned to 4 or 8 cores (which will increase the memory as well). ---
**Author:** ![sph17](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/sph17/32/684_2.png) [@sph17](https://discuss.hail.is/u/sph17)\ **Post date:** [December 3, 2021, 6:31pm UTC](https://discuss.hail.is/t/java-error-message-when-writing-output-in-hail/2391/5 "2021-12-03T18:31:16Z")
Okay I will give that a shot, the VCF is only 5000 lines, I was just testing out the script. Let me give that a try! ---
**Author:** ![sph17](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/sph17/32/684_2.png) [@sph17](https://discuss.hail.is/u/sph17)\ **Post date:** [December 3, 2021, 7:07pm UTC](https://discuss.hail.is/t/java-error-message-when-writing-output-in-hail/2391/6 "2021-12-03T19:07:13Z")
@tpoterba Memory increase fixed the issue if I write it locally, but the file does not exist ```auto SparkUI available at http://saturn-282f6108-da43-4df8-95ea-903fb699127b-m.c.terra-2d3a4d00.internal:4040 Welcome to ____ <>__ / /_/ / ____ / / / __ / _ `/ / / /_/ /_/\_,_/_/_/ version 0.2.62-84fa81b9ea3d LOGGING: writing to /home/jupyter/hail-20211203-1940-0.2.62-84fa81b9ea3d.log 2021-12-03 19:41:03 Hail: INFO: Reading table without type imputation Loading field 'f0' as type str (user-supplied) Loading field 'f1' as type int32 (user-supplied) Loading field 'f2' as type int32 (user-supplied) 2021-12-03 19:41:03 Hail: INFO: Reading table without type imputation Loading field 'SampleID' as type str (not specified) Loading field 'FamID' as type str (not specified) Loading field 'Role' as type str (not specified) 2021-12-03 19:41:23 Hail: INFO: Coerced sorted dataset 2021-12-03 19:41:26 Hail: WARN: entries(): Resulting entries table is sorted by '(row_key, col_key)'. To preserve row-major matrix table order, first unkey columns with 'key_cols_by()' 2021-12-03 19:41:26 Hail: INFO: Reading table without type imputation Loading field 'FamID' as type str (not specified) Loading field 'TrioID' as type str (not specified) Loading field 'SampleID' as type str (not specified) Loading field 'FatherID' as type str (not specified) Loading field 'MotherID' as type str (not specified) 2021-12-03 19:41:27 Hail: WARN: export_vcf: ignored the following fields: 'pheno' (column) 'num_alleles' (row) 'a_index' (row) 'was_split' (row) 2021-12-03 19:41:43 Hail: INFO: Coerced sorted dataset 2021-12-03 19:41:55 Hail: INFO: Coerced sorted dataset 2021-12-03 19:42:32 Hail: INFO: Coerced sorted dataset 2021-12-03 19:42:41 Hail: INFO: Coerced sorted dataset 2021-12-03 19:42:51 Hail: INFO: Coerced sorted dataset 2021-12-03 19:43:15 Hail: INFO: Coerced sorted dataset 2021-12-03 19:43:28 Hail: INFO: Coerced sorted dataset 2021-12-03 19:43:37 Hail: INFO: Coerced sorted dataset 2021-12-03 19:44:00 Hail: INFO: Coerced sorted dataset 2021-12-03 19:44:27 Hail: INFO: Ordering unsorted dataset with network shuffle 2021-12-03 19:44:27 Hail: INFO: Ordering unsorted dataset with network shuffle 2021-12-03 19:44:44 Hail: INFO: Ordering unsorted dataset with network shuffle 2021-12-03 19:45:55 Hail: INFO: merging 1 files totalling 45.8K... 2021-12-03 19:45:55 Hail: INFO: while writing: mssng_db6.chr12_filter_ME_v3_loosefilters.vcf.bgz merge time: 131.775ms Processing:12 ``` But doesn’t exist: ```auto jupyter@saturn-282f6108-da43-4df8-95ea-903fb699127b-m:~$ ls hail-20211203-1859-0.2.62-84fa81b9ea3d.log notebooks hail-20211203-1912-0.2.62-84fa81b9ea3d.log stdout.txt hail-20211203-1931-0.2.62-84fa81b9ea3d.log wgs_pre_processing_vcf_v3_Loose_Filters.py hail-20211203-1940-0.2.62-84fa81b9ea3d.log ``` ---
**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\ **Post date:** [December 3, 2021, 7:49pm UTC](https://discuss.hail.is/t/java-error-message-when-writing-output-in-hail/2391/7 "2021-12-03T19:49:45Z")
I’m not sure what the default working directory is for Terra. You might try writing to an explicit full path rather than relative. ---
**Author:** ![sph17](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/sph17/32/684_2.png) [@sph17](https://discuss.hail.is/u/sph17)\ **Post date:** [December 3, 2021, 8:31pm UTC](https://discuss.hail.is/t/java-error-message-when-writing-output-in-hail/2391/8 "2021-12-03T20:31:06Z")
When I tried with explicit paths either locally /home/jupyter/ or uri gs://google/bucket, I get thrown the same java error as above… Not sure what’s going on here.