Having issue to run an analys (fastq doesn't appear to be under any mount points)

• 

  Jason Cerrato

  • December 02, 2025 17:45

  Hi Lingwood Lab,

  Thank you for reaching out. Terra has changed in numerous ways since 2023, so it's possible that something has changed since your script was last run. When did you last run it successfully?

  Can you share more details about how you are running the script? Is it through a cloud environment or via a WDL submission? 

  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 a link to your workspace, as well as information on where to find the error you saw, and we will be happy to take a closer look.

  Kind regards,

  Jason

  0
• 

  Lingwood Lab

  • December 03, 2025 15:17

  Dear Jason, thank you for your reply. I lunched my last analysis on 31st May 2024 and the script and analysis worked well. I run the script via Terra (github.com/ShalekLab/ampliconBCR/ampliconBCR_solo:main) and I uploaded all my data and sample sheets in our allocated bucket in google cloud (https://storage.cloud.google.com/fc-55635fd2-b649-40d6-b08b-011840c8414c/)

  I have shared the workspace so that You will have acces to it.

  Here is the log of the error that I am getting ultimately, when analyzing these data (https://storage.cloud.google.com/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR_Mehak1) 

  Thank you very much for you help.

  Best,
  Faez

  2025-12-01 20:15:08,493 INFO - MaterializeWorkflowDescriptorActor [UUID(7878410c)]: Parsing workflow as WDL 1.0 2025-12-01 20:15:08,502 INFO - MaterializeWorkflowDescriptorActor [UUID(7878410c)]: Call-to-Backend assignments: amplicon_BCR_alignment.migmap -> GCPBatch, amplicon_BCR_alignment.panda_express -> GCPBatch, amplicon_BCR_alignment.consensus -> GCPBatch 2025-12-01 20:15:12,849 INFO - WorkflowExecutionActor-7878410c-8ba1-496d-bcf5-646ab1e727ec [UUID(7878410c)]: Starting amplicon_BCR_alignment.panda_express (10 shards) 2025-12-01 20:15:13,870 INFO - WorkflowExecutionActor-7878410c-8ba1-496d-bcf5-646ab1e727ec [UUID(7878410c)]: Starting amplicon_BCR_alignment.panda_express (278 shards) 2025-12-01 20:15:15,119 INFO - 7878410c-8ba1-496d-bcf5-646ab1e727ec-EngineJobExecutionActor-amplicon_BCR_alignment.panda_express:287:1 [UUID(7878410c)]: Could not copy a suitable cache hit for {7878410c:amplicon_BCR_alignment.panda_express:287:1}. No copy attempts were made. 2025-12-01 20:15:15,120 INFO - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:287:1]: `set -e mkdir -p /cromwell_root/out/ cd /cromwell_root/out/ pandaseq -F \ -f /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0288_S288_L001_R1_001.fastq.gz \ -r /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0288_S288_L001_R2_001.fastq.gz \ -w S0288_paired.fastq \ -g S0288_pandaseq.log \ -l 200 \ -T 4 ls echo "Panda-Seq is done, produced S0288_paired.fastq. Read S0288_pandaseq.log for more details."` 2025-12-01 20:15:15,163 INFO - 7878410c-8ba1-496d-bcf5-646ab1e727ec-EngineJobExecutionActor-amplicon_BCR_alignment.panda_express:42:1 [UUID(7878410c)]: Could not copy a suitable cache hit for {7878410c:amplicon_BCR_alignment.panda_express:42:1}. No copy attempts were made. 2025-12-01 20:15:15,164 INFO - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:42:1]: `set -e mkdir -p /cromwell_root/out/ cd /cromwell_root/out/ pandaseq -F \ -f /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0043_S43_L001_R1_001.fastq.gz \ -r /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0043_S43_L001_R2_001.fastq.gz \ -w S0043_paired.fastq \ -g S0043_pandaseq.log \ -l 200 \ -T 4 ls echo "Panda-Seq is done, produced S0043_paired.fastq. Read S0043_pandaseq.log for more details."` 2025-12-01 20:15:15,209 INFO - 7878410c-8ba1-496d-bcf5-646ab1e727ec-EngineJobExecutionActor-amplicon_BCR_alignment.panda_express:38:1 [UUID(7878410c)]: Could not copy a suitable cache hit for {7878410c:amplicon_BCR_alignment.panda_express:38:1}. No copy attempts were made. 2025-12-01 20:15:15,210 INFO - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:38:1]: `set -e mkdir -p /cromwell_root/out/ cd /cromwell_root/out/ pandaseq -F \ -f /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0039_S39_L001_R1_001.fastq.gz \ -r /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0039_S39_L001_R2_001.fastq.gz \ -w S0039_paired.fastq \ -g S0039_pandaseq.log \ -l 200 \ -T 4 ls echo "Panda-Seq is done, produced S0039_paired.fastq. Read S0039_pandaseq.log for more details."` 2025-12-01 20:15:15,254 INFO - 7878410c-8ba1-496d-bcf5-646ab1e727ec-EngineJobExecutionActor-amplicon_BCR_alignment.panda_express:245:1 [UUID(7878410c)]: Could not copy a suitable cache hit for {7878410c:amplicon_BCR_alignment.panda_express:245:1}. No copy attempts were made. 2025-12-01 20:15:15,256 INFO - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:245:1]: `set -e mkdir -p /cromwell_root/out/ cd /cromwell_root/out/ pandaseq -F \ -f /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0246_S246_L001_R1_001.fastq.gz \ -r /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0246_S246_L001_R2_001.fastq.gz \ -w S0246_paired.fastq \ -g S0246_pandaseq.log \ -l 200 \ -T 4 ls echo "Panda-Seq is done, produced S0246_paired.fastq. Read S0246_pandaseq.log for more details."` 2025-12-01 20:15:15,271 ERROR - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:287:1]: Error attempting to Execute java.lang.Exception: Absolute path /cromwell_root/out/S0288_paired.fastq doesn't appear to be under any mount points: local-disk 128 HDD at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.relativePathAndAttachedDisk(GcpBatchAsyncBackendJobExecutionActor.scala:721) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateSingleFileOutputs(GcpBatchAsyncBackendJobExecutionActor.scala:828) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$generateOutputs$8(GcpBatchAsyncBackendJobExecutionActor.scala:863) at scala.collection.immutable.List.flatMap(List.scala:293) at scala.collection.immutable.List.flatMap(List.scala:79) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$generateOutputs$7(GcpBatchAsyncBackendJobExecutionActor.scala:860) at scala.collection.immutable.List.flatMap(List.scala:293) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateOutputs(GcpBatchAsyncBackendJobExecutionActor.scala:859) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$executeAsync$2(GcpBatchAsyncBackendJobExecutionActor.scala:974) at scala.util.Try$.apply(Try.scala:210) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateInputOutputParameters$1(GcpBatchAsyncBackendJobExecutionActor.scala:927) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$executeAsync$8(GcpBatchAsyncBackendJobExecutionActor.scala:988) at scala.concurrent.impl.Promise$Transformation.run(Promise.scala:470) at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:41) at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:49) at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107) 2025-12-01 20:15:15,303 ERROR - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:42:1]: Error attempting to Execute java.lang.Exception: Absolute path /cromwell_root/out/S0043_paired.fastq doesn't appear to be under any mount points: local-disk 128 HDD at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.relativePathAndAttachedDisk(GcpBatchAsyncBackendJobExecutionActor.scala:721) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateSingleFileOutputs(GcpBatchAsyncBackendJobExecutionActor.scala:828) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$generateOutputs$8(GcpBatchAsyncBackendJobExecutionActor.scala:863) at scala.collection.immutable.List.flatMap(List.scala:293) at scala.collection.immutable.List.flatMap(List.scala:79) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$generateOutputs$7(GcpBatchAsyncBackendJobExecutionActor.scala:860) at scala.collection.immutable.List.flatMap(List.scala:293) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateOutputs(GcpBatchAsyncBackendJobExecutionActor.scala:859) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$executeAsync$2(GcpBatchAsyncBackendJobExecutionActor.scala:974) at scala.util.Try$.apply(Try.scala:210) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateInputOutputParameters$1(GcpBatchAsyncBackendJobExecutionActor.scala:927) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$executeAsync$8(GcpBatchAsyncBackendJobExecutionActor.scala:988) at scala.concurrent.impl.Promise$Transformation.run(Promise.scala:470) at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:41) at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:49) at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107) 2025-12-01 20:15:15,343 ERROR - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:38:1]: Error attempting to Execute java.lang.Exception: Absolute path /cromwell_root/out/S0039_paired.fastq doesn't appear to be under any mount points: local-disk 128 HDD at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.relativePathAndAttachedDisk(GcpBatchAsyncBackendJobExecutionActor.scala:721) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateSingleFileOutputs(GcpBatchAsyncBackendJobExecutionActor.scala:828) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$generateOutputs$8(GcpBatchAsyncBackendJobExecutionActor.scala:863) at scala.collection.immutable.List.flatMap(List.scala:293) at scala.collection.immutable.List.flatMap(List.scala:79) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$generateOutputs$7(GcpBatchAsyncBackendJobExecutionActor.scala:860) at scala.collection.immutable.List.flatMap(List.scala:293) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateOutputs(GcpBatchAsyncBackendJobExecutionActor.scala:859) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$executeAsync$2(GcpBatchAsyncBackendJobExecutionActor.scala:974) at scala.util.Try$.apply(Try.scala:210) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateInputOutputParameters$1(GcpBatchAsyncBackendJobExecutionActor.scala:927) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$executeAsync$8(GcpBatchAsyncBackendJobExecutionActor.scala:988) at scala.concurrent.impl.Promise$Transformation.run(Promise.scala:470) at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:41) at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:49) at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107) 2025-12-01 20:15:15,408 ERROR - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:245:1]: Error attempting to Execute java.lang.Exception: Absolute path /cromwell_root/out/S0246_paired.fastq doesn't appear to be under any mount points: local-disk 128 HDD at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.relativePathAndAttachedDisk(GcpBatchAsyncBackendJobExecutionActor.scala:721) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateSingleFileOutputs(GcpBatchAsyncBackendJobExecutionActor.scala:828) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$generateOutputs$8(GcpBatchAsyncBackendJobExecutionActor.scala:863) at scala.collection.immutable.List.flatMap(List.scala:293) at scala.collection.immutable.List.flatMap(List.scala:79) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$generateOutputs$7(GcpBatchAsyncBackendJobExecutionActor.scala:860) at scala.collection.immutable.List.flatMap(List.scala:293) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateOutputs(GcpBatchAsyncBackendJobExecutionActor.scala:859) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$executeAsync$2(GcpBatchAsyncBackendJobExecutionActor.scala:974) at scala.util.Try$.apply(Try.scala:210) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateInputOutputParameters$1(GcpBatchAsyncBackendJobExecutionActor.scala:927) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$executeAsync$8(GcpBatchAsyncBackendJobExecutionActor.scala:988) at scala.concurrent.impl.Promise$Transformation.run(Promise.scala:470) at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:41) at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:49) at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107) 2025-12-01 20:15:19,016 INFO - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:42:1]: `set -e mkdir -p /cromwell_root/out/ cd /cromwell_root/out/ pandaseq -F \ -f /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0043_S43_L001_R1_001.fastq.gz \ -r /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0043_S43_L001_R2_001.fastq.gz \ -w S0043_paired.fastq \ -g S0043_pandaseq.log \ -l 200 \ -T 4 ls echo "Panda-Seq is done, produced S0043_paired.fastq. Read S0043_pandaseq.log for more details."` 2025-12-01 20:15:19,273 ERROR - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:42:1]: Error attempting to Execute java.lang.Exception: Absolute path /cromwell_root/out/S0043_paired.fastq doesn't appear to be under any mount points: local-disk 128 HDD at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.relativePathAndAttachedDisk(GcpBatchAsyncBackendJobExecutionActor.scala:721) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateSingleFileOutputs(GcpBatchAsyncBackendJobExecutionActor.scala:828) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$generateOutputs$8(GcpBatchAsyncBackendJobExecutionActor.scala:863) at scala.collection.immutable.List.flatMap(List.scala:293) at scala.collection.immutable.List.flatMap(List.scala:79) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$generateOutputs$7(GcpBatchAsyncBackendJobExecutionActor.scala:860) at scala.collection.immutable.List.flatMap(List.scala:293) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateOutputs(GcpBatchAsyncBackendJobExecutionActor.scala:859) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$executeAsync$2(GcpBatchAsyncBackendJobExecutionActor.scala:974) at scala.util.Try$.apply(Try.scala:210) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateInputOutputParameters$1(GcpBatchAsyncBackendJobExecutionActor.scala:927) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$executeAsync$8(GcpBatchAsyncBackendJobExecutionActor.scala:988) at scala.concurrent.impl.Promise$Transformation.run(Promise.scala:470) at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:41) at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:49) at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107) 2025-12-01 20:15:21,075 INFO - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:287:1]: `set -e mkdir -p /cromwell_root/out/ cd /cromwell_root/out/ pandaseq -F \ -f /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0288_S288_L001_R1_001.fastq.gz \ -r /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0288_S288_L001_R2_001.fastq.gz \ -w S0288_paired.fastq \ -g S0288_pandaseq.log \ -l 200 \ -T 4 ls echo "Panda-Seq is done, produced S0288_paired.fastq. Read S0288_pandaseq.log for more details."` 2025-12-01 20:15:21,284 ERROR - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:287:1]: Error attempting to Execute java.lang.Exception: Absolute path /cromwell_root/out/S0288_paired.fastq doesn't appear to be under any mount points: local-disk 128 HDD at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.relativePathAndAttachedDisk(GcpBatchAsyncBackendJobExecutionActor.scala:721) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateSingleFileOutputs(GcpBatchAsyncBackendJobExecutionActor.scala:828) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$generateOutputs$8(GcpBatchAsyncBackendJobExecutionActor.scala:863) at scala.collection.immutable.List.flatMap(List.scala:293) at scala.collection.immutable.List.flatMap(List.scala:79) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$generateOutputs$7(GcpBatchAsyncBackendJobExecutionActor.scala:860) at scala.collection.immutable.List.flatMap(List.scala:293) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateOutputs(GcpBatchAsyncBackendJobExecutionActor.scala:859) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$executeAsync$2(GcpBatchAsyncBackendJobExecutionActor.scala:974) at scala.util.Try$.apply(Try.scala:210) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.generateInputOutputParameters$1(GcpBatchAsyncBackendJobExecutionActor.scala:927) at cromwell.backend.google.batch.actors.GcpBatchAsyncBackendJobExecutionActor.$anonfun$executeAsync$8(GcpBatchAsyncBackendJobExecutionActor.scala:988) at scala.concurrent.impl.Promise$Transformation.run(Promise.scala:470) at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:41) at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:49) at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107) 2025-12-01 20:15:21,635 INFO - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:38:1]: `set -e mkdir -p /cromwell_root/out/ cd /cromwell_root/out/ pandaseq -F \ -f /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0039_S39_L001_R1_001.fastq.gz \ -r /mnt/disks/cromwell_root/fc-55635fd2-b649-40d6-b08b-011840c8414c/BCR83_d14_LC/S0039_S39_L001_R2_001.fastq.gz \ -w S0039_paired.fastq \ -g S0039_pandaseq.log \ -l 200 \ -T 4 ls echo "Panda-Seq is done, produced S0039_paired.fastq. Read S0039_pandaseq.log for more details."` 2025-12-01 20:15:21,857 ERROR - GcpBatchAsyncBackendJobExecutionActor [UUID(7878410c)amplicon_BCR_alignment.panda_express:38:1]: Error attempting to Execute java.lang.Exception: Absolute path /cromwell

  0
• 

  Jason Cerrato

  • December 04, 2025 16:19

  Hello,

  Thank you for those details. The Google Cloud API for running workflows has changed since you last ran your script, which might be the reason why the script is now failing. See: Cromwell on Google Batch API - released May 19, Generally Available as of June 23

  Here are the recommendations for how to resolve your issue:

  • Remove the explicit cd and mkdir: The command block should run its primary tool directly in the /cromwell_root directory.

  • Adjust the output file paths: Since the files are being written to the out/ subdirectory, the output block must correctly reference this subdirectory.

  You can try this revised WDL code for the command and output blocks:

  command <<<
         set -e
         # 1. FIX: Create the 'out/' directory relative to the current working directory (/cromwell_root)
         mkdir -p out/ 
         
         # 2. FIX: Write the output files directly into the 'out/' subdirectory
         pandaseq -F \
            -f ~{fastq_R1} \
            -r ~{fastq_R2} \
            -w out/~{paired_fastq} \
            -g out/~{log} \
            -l ~{minimum_read_length} \
            -T ~{number_cpu_threads}
            
         ls out/
         echo "Panda-Seq is done, produced ~{paired_fastq}. Read ~{log} for more details."
      >>>
      output {
         # 3. FIX: Reference the file path relative to /cromwell_root. Cromwell finds it!
         Pair[String, File] sample_paired_fastq = (sample_name, "out/~{paired_fastq}") 
         File pandaseq_log = "out/~{log}"
      }

  Kind regards,

  Jason

  0

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