Workflow Fail/Error in "Copying" files in workflow log

Post author
Chloe Tu

My test workflow loads in data, but continues to fail due to an error in copying the files called. How can I fix the copying error? The files are successfully initialized in the log, in some lines beforehand.

Thanks!

An example of the error code:

[batch_task_logs]2025/06/20 17:43:56 ERROR: [task_id:task/job-d816fac9-3a24-dd06bf95-cc89-49c700-group0-0/0/0,runnable_index:8] Copying gs://fc-secure-6c917763-0f6d-47bf-9cd9-23b033843e8b/references/Mus_musculus.GRCm38.dna.primary_assembly.fasta to file:///mnt/disks/cromwell_root/fc-secure-6c917763-0f6d-47bf-9cd9-23b033843e8b/references/Mus_musculus.GRCm38.dna.primary_assembly.fasta
[batch_task_logs]2025/06/20 17:43:56 ERROR: [task_id:task/job-d816fac9-3a24-dd06bf95-cc89-49c700-group0-0/0/0,runnable_index:8] Copying gs://fc-secure-6c917763-0f6d-47bf-9cd9-23b033843e8b/references/Mus_musculus.GRCm38.dna.primary_assembly.fa.amb to file:///mnt/disks/cromwell_root/fc-secure-6c917763-0f6d-47bf-9cd9-23b033843e8b/references/Mus_musculus.GRCm38.dna.primary_assembly.fa.amb

 

My test workflow:

version 1.0

struct Runtime {
	Int max_retries
	Int preemptible
	Int mem
	Int cpu
	Int boot_disk_size # must be big enough to store the Docker image
	Int initial_disk_size # padding for disk
}

workflow bwaMem {
	input {
		File ref_fasta
		File read1
		File read2

		File ref_amb
		File ref_ann
		File ref_sa
		File ref_pac
		File ref_bwt
		
		String bwa_docker = "broadinstitute/genomes-in-the-cloud:2.3.1-1512499786"
	}
	
	call bwaMem {
		input:
			read1 = read1,
			read2 = read2,
			ref_sa = ref_sa,
			ref_ann = ref_ann,
			ref_bwt = ref_bwt,
			ref_pac = ref_pac,
			ref_amb = ref_amb,
			ref_fasta = ref_fasta,

			preemptible = 1,
			max_retries = 0,
			boot_disk_size = 15, # GATK magic number
			initial_mem = 15,
			initial_disk_size = 15,
			cpu = 8,
			docker_path = bwa_docker
		}
}

task bwaMem {
	input {
		File read1
		File read2
		File ref_amb
		File ref_ann
		File ref_bwt
		File ref_fasta
		File ref_pac
		File ref_sa
		String docker_path
		# Optional runtime variables (>= 16 GB RAM recommended)
		Int preemptible
		Int boot_disk_size
		Int max_retries
		Int initial_mem
		Int initial_disk_size
		Int cpu 
	}

	Int disk_gb = initial_disk_size 
	Int mem = initial_mem 

	String ref_prefix = basename(ref_fasta)

	command <<<
		echo "TEST"
	>>>

	runtime {
		docker : docker_path
		bootDiskSizeGb: boot_disk_size
		preemptible: preemptible
		cpu: cpu
		disks: "local-disk " + disk_gb + " HDD"
		memory: mem + "GB"
		maxRetries: max_retries
	}
}

Comments

1 comment

  • Comment author
    Samantha (she/her)

    Hi Chloe,

    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,

    Samantha

    0

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