Delocalization of output failing for successful alignment

Post author
Lab JLanders

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

  • Comment author
    Josh Evans

    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.

    1. Toggle the "Share with support" button to "Yes"
    2. Click Save

    Please provide us with

    1. A link to your workspace
    2. The relevant submission ID
    3. The relevant workflow ID

    We’ll be happy to take a closer look as soon as we can!

    Kind regards,

    Josh

    0
  • Comment author
    Lab JLanders

    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!

     

    0

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