Workflow Fail/Error in "Copying" files in workflow log
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
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.
Please provide us with
We’ll be happy to take a closer look as soon as we can!
Kind regards,
Samantha
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