Delocalization of output failing for successful alignment
I have created a short WDL script to use STAR aligner to create bam files from fastq files. The workflow is giving me an error. Here is the log file of the workflow:
2023/03/29 19:53:19 Starting container setup. 2023/03/29 19:53:21 Done container setup. 2023/03/29 19:53:22 Starting localization. 2023/03/29 19:53:30 Localization script execution started... 2023/03/29 19:53:30 Localizing input gs://fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/star_index/hg38.tar.gz -> /cromwell_root/fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/star_index/hg38.tar.gz 2023/03/29 20:00:11 Localizing input gs://fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/487f9982-982f-4f85-9a1e-d537fd4949e9/star_workflow/0486f54d-eed0-40d0-9fea-629f7339a7e5/call-star/script -> /cromwell_root/script 2023/03/29 20:00:13 Localizing input gs://fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/440ef419-6c63-4c59-8970-c3ee2a1e903e/umitools_extract/e74811e6-4482-4af6-9d53-a5269765c90d/call-extract1/22c_R1.extract.fastq.gz -> /cromwell_root/fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/440ef419-6c63-4c59-8970-c3ee2a1e903e/umitools_extract/e74811e6-4482-4af6-9d53-a5269765c90d/call-extract1/22c_R1.extract.fastq.gz 2023/03/29 20:00:15 Localizing input gs://fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/440ef419-6c63-4c59-8970-c3ee2a1e903e/umitools_extract/e74811e6-4482-4af6-9d53-a5269765c90d/call-extract2/22c_R2.extract.fastq.gz -> /cromwell_root/fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/440ef419-6c63-4c59-8970-c3ee2a1e903e/umitools_extract/e74811e6-4482-4af6-9d53-a5269765c90d/call-extract2/22c_R2.extract.fastq.gz 2023/03/29 20:00:17 Localization script execution complete. 2023/03/29 20:00:21 Done localization. 2023/03/29 20:00:22 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint=/bin/bash alexdobin/star@sha256:32eb10351954db2cdd5ea4c9ab4621ca7fa11feeb395411e5bc3aa27593caa6c /cromwell_root/script FASTQs: /cromwell_root/fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/440ef419-6c63-4c59-8970-c3ee2a1e903e/umitools_extract/e74811e6-4482-4af6-9d53-a5269765c90d/call-extract1/22c_R1.extract.fastq.gz /cromwell_root/fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/440ef419-6c63-4c59-8970-c3ee2a1e903e/umitools_extract/e74811e6-4482-4af6-9d53-a5269765c90d/call-extract2/22c_R2.extract.fastq.gz [Mar 29 20:00:23] Extracting STAR index -rw-r--r-- root/root 25156855213 2023-03-27 21:04 hg38/SA -rw-r--r-- root/root 732 2023-03-27 21:03 hg38/genomeParameters.txt -rw-r--r-- root/root 3021 2023-03-27 15:42 hg38/chrLength.txt -rw-r--r-- root/root 8716 2023-03-27 15:42 hg38/chrNameLength.txt -rw-r--r-- root/root 4990 2023-03-27 15:42 hg38/chrStart.txt -rw-r--r-- root/root 1565873619 2023-03-27 21:04 hg38/SAindex -rw-r--r-- root/root 84018 2023-03-27 21:04 hg38/Log.out -rw-r--r-- root/root 3279945728 2023-03-27 21:03 hg38/Genome -rw-r--r-- root/root 5695 2023-03-27 15:42 hg38/chrName.txt STAR --genomeDir star_index --twopassMode Basic --outSAMtype BAM SortedByCoordinate --readFilesIn /cromwell_root/fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/440ef419-6c63-4c59-8970-c3ee2a1e903e/umitools_extract/e74811e6-4482-4af6-9d53-a5269765c90d/call-extract1/22c_R1.extract.fastq.gz /cromwell_root/fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/440ef419-6c63-4c59-8970-c3ee2a1e903e/umitools_extract/e74811e6-4482-4af6-9d53-a5269765c90d/call-extract2/22c_R2.extract.fastq.gz --outFileNamePrefix ./star_put/22c --readFilesCommand zcat STAR version: 2.7.10a compiled: 2022-05-11T17:42:47+00:00 cb5d3616d6c5:/home/STAR-2.7.10a/source Mar 29 20:03:37 ..... started STAR run Mar 29 20:03:38 ..... loading genome Mar 29 20:03:58 ..... started 1st pass mapping Mar 29 20:07:14 ..... finished 1st pass mapping Mar 29 20:07:14 ..... inserting junctions into the genome indices Mar 29 20:08:47 ..... started mapping Mar 29 20:16:27 ..... finished mapping Mar 29 20:16:30 ..... started sorting BAM Mar 29 20:16:43 ..... finished successfully 2023/03/29 20:16:45 Starting delocalization. 2023/03/29 20:16:46 Delocalization script execution started... 2023/03/29 20:16:46 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/487f9982-982f-4f85-9a1e-d537fd4949e9/star_workflow/0486f54d-eed0-40d0-9fea-629f7339a7e5/call-star/memory_retry_rc 2023/03/29 20:16:48 Delocalizing output /cromwell_root/rc -> gs://fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/487f9982-982f-4f85-9a1e-d537fd4949e9/star_workflow/0486f54d-eed0-40d0-9fea-629f7339a7e5/call-star/rc 2023/03/29 20:16:50 Delocalizing output /cromwell_root/stdout -> gs://fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/487f9982-982f-4f85-9a1e-d537fd4949e9/star_workflow/0486f54d-eed0-40d0-9fea-629f7339a7e5/call-star/stdout 2023/03/29 20:16:51 Delocalizing output /cromwell_root/stderr -> gs://fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/487f9982-982f-4f85-9a1e-d537fd4949e9/star_workflow/0486f54d-eed0-40d0-9fea-629f7339a7e5/call-star/stderr 2023/03/29 20:16:53 Delocalizing output /cromwell_root/star_out/22c.Aligned.sortedByCoord.out.bam -> gs://fc-secure-e7fe088f-805c-48a7-8e04-84732ca97435/submissions/487f9982-982f-4f85-9a1e-d537fd4949e9/star_workflow/0486f54d-eed0-40d0-9fea-629f7339a7e5/call-star/star_out/22c.Aligned.sortedByCoord.out.bam Required file output '/cromwell_root/star_out/22c.Aligned.sortedByCoord.out.bam' does not exist.
As you can see, the STAR alignment finished successfully but the output of the command was not able to be found when delocalized. If anyone knows why this is, please let me know.
Comments
2 comments
Hi,
Thank you for writing in about this issue! Can you share the workspace where you are seeing this issue with Terra Support by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.
Please provide us with
We’ll be happy to take a closer look as soon as we can!
Kind regards,
Josh
Hello,
Here is the link to the workspace:
https://app.terra.bio/#workspaces/als-data-project/VCF-tools
Here is the submission ID:
487f9982-982f-4f85-9a1e-d537fd4949e9
Here is the google could ID:
0486f54d-eed0-40d0-9fea-629f7339a7e5
Thanks!
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