# Too many arguments on the command line **URL:** \ **Category:** CWL Questions\ **Created:** [December 2, 2020, 9:36am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248 "2020-12-02T09:36:30Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![matmanc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/matmanc/32/113_2.png) [@matmanc](https://cwl.discourse.group/u/matmanc)\ **Post date:** [December 2, 2020, 9:36am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/1 "2020-12-02T09:36:30Z")
Hi all, I am using CWL version 1.0 to describe both the steps and the workflow. If I use as input to a step and I put a directory array (Directory[]) and I run the workflow with singularity it happens that if the file list is too long I get a Too many arguments on the command line. I am currently running the workflow with Toil. Is there a way around this problem? Thank you, Mattia ---
**Author:** ![mrc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/mrc/32/3_2.png) [@mrc](https://cwl.discourse.group/u/mrc)\ **Post date:** [December 2, 2020, 10:05am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/2 "2020-12-02T10:05:04Z")
Welcome @matmanc! Can you share the CWL tool description you are using and what happens with you execute it using the CWL reference runner, `cwltool`? (Or an excerpt from your `toil-cwl-runner` logs) ---
**Author:** ![matmanc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/matmanc/32/113_2.png) [@matmanc](https://cwl.discourse.group/u/matmanc)\ **Post date:** [December 2, 2020, 10:12am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/3 "2020-12-02T10:12:35Z")
sure here is the tool description: ``` class: CommandLineTool cwlVersion: v1.0 id: check_ateam_separation baseCommand: - python3 - /usr/local/bin/check_Ateam_separation.py inputs: - id: ms type: - Directory - type: array items: Directory inputBinding: position: 0 doc: Input measurement set - default: Ateam_separation.png id: output_image_name type: string? inputBinding: position: 2 prefix: '--outputimage' - id: min_separation type: int inputBinding: position: 1 prefix: '--min_separation' outputs: - id: output_imag doc: Output image type: File? outputBinding: glob: $(inputs.output_image_name) - id: logfile type: File? outputBinding: glob: Ateam_separation.log label: check_Ateam_separation hints: - class: DockerRequirement dockerPull: lofareosc/prefactor:HBAcalibrator - class: InlineJavascriptRequirement stdout: Ateam_separation.log ``` unfortunately I didnt save the log so I will paste it here soon. The problem was on the line that singularity binds every single file in every single directory resulting in a very long command line that generates a os error as the number of arguments is limited by the kernel. ---
**Author:** ![matmanc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/matmanc/32/113_2.png) [@matmanc](https://cwl.discourse.group/u/matmanc)\ **Post date:** [December 2, 2020, 10:26am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/4 "2020-12-02T10:26:06Z")
Here it is ``` [2020-12-02T11:21:48+0100] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'file:///project/astroneosc/Software/prefactor3-cwl/lofar-cwl/steps /check_ateam_separation.cwl#check_ateam_separation' python3 /usr/local/bin/check_Ateam_separation.py kind-file_project_astroneosc_Software_prefactor3-cwl_lofar-cwl_steps_check_ateam_se paration.cwl_check_ateam_separation/instance-r0brc7sq [2020-12-02T11:21:48+0100] [MainThread] [W] [toil.leader] Log from job kind-file_project_astroneosc_Software_prefactor3-cwl_lofar-cwl_steps_check_ateam_separation.cwl_check_ateam_separ ation/instance-r0brc7sq follows: =========> /table.dat:ro \ --bind \ /project/astroneosc/Data/tmp/node-70e26f65-197b-49f9-90aa-52b42e8d7822-4b184c8e-e9fd-4784-92c4-5ace3fd7ef2c/tmp074diqpq/31cdf995-536c-4d07-9b48-c72e6df42315/tmpsvnitjnw.tmp :/var/lib/cwl/stga6073e5c-0ba5-472f-9790-6480440e0258/L755125_SB222_uv.MS/table.f4_TSM0:ro \ --bind \ /project/astroneosc/Data/tmp/node-70e26f65-197b-49f9-90aa-52b42e8d7822-4b184c8e-e9fd-4784-92c4-5ace3fd7ef2c/tmp074diqpq/31cdf995-536c-4d07-9b48-c72e6df42315/tmpfw7whow7.tmp :/var/lib/cwl/stga6073e5c-0ba5-472f-9790-6480440e0258/L755125_SB222_uv.MS/DATA_DESCRIPTION/table.info:ro \ --bind \ /project/astroneosc/Data/tmp/node-70e26f65-197b-49f9-90aa-52b42e8d7822-4b184c8e-e9fd-4784-92c4-5ace3fd7ef2c/tmp074diqpq/31cdf995-536c-4d07-9b48-c72e6df42315/tmp1o7zp770.tmp :/var/lib/cwl/stga6073e5c-0ba5-472f-9790-6480440e0258/L755125_SB222_uv.MS/DATA_DESCRIPTION/table.f0:ro \ --bind \ /project/astroneosc/Data/tmp/node-70e26f65-197b-49f9-90aa-52b42e8d7822-4b184c8e-e9fd-4784-92c4-5ace3fd7ef2c/tmp074diqpq/31cdf995-536c-4d07-9b48-c72e6df42315/tmp8clmv0ww.tmp :/var/lib/cwl/stga6073e5c-0ba5-472f-9790-6480440e0258/L755125_SB222_uv.MS/DATA_DESCRIPTION/table.dat:ro \ --bind \ /project/astroneosc/Data/tmp/node-70e26f65-197b-49f9-90aa-52b42e8d7822-4b184c8e-e9fd-4784-92c4-5ace3fd7ef2c/tmp074diqpq/31cdf995-536c-4d07-9b48-c72e6df42315/tmpj09nien5.tmp :/var/lib/cwl/stga6073e5c-0ba5-472f-9790-6480440e0258/L755125_SB222_uv.MS/table.f0:ro \ --bind \ /project/astroneosc/Data/tmp/node-70e26f65-197b-49f9-90aa-52b42e8d7822-4b184c8e-e9fd-4784-92c4-5ace3fd7ef2c/tmp074diqpq/31cdf995-536c-4d07-9b48-c72e6df42315/tmpnmj0wmwj.tmp :/var/lib/cwl/stga6073e5c-0ba5-472f-9790-6480440e0258/L755125_SB222_uv.MS/QUALITY_FREQUENCY_STATISTIC/table.info:ro \ --bind \ /project/astroneosc/Data/tmp/node-70e26f65-197b-49f9-90aa-52b42e8d7822-4b184c8e-e9fd-4784-92c4-5ace3fd7ef2c/tmp074diqpq/31cdf995-536c-4d07-9b48-c72e6df42315/tmp3xtw2kh7.tmp [...] --pwd \ /vWWYEQ \ /project/astroneosc/Software/prefactor3.simg \ python3 \ /usr/local/bin/check_Ateam_separation.py \ /var/lib/cwl/stg7dbf09a8-5fa9-48ed-b4c2-fe2eb29f266a/L755125_SB000_uv.MS \ /var/lib/cwl/stgf721eb4f-99dd-4b87-8fe6-9e250a7317ce/L755125_SB002_uv.MS \ /var/lib/cwl/stg5b01d833-66e4-4dcd-9877-d33c7b7cd5b9/L755125_SB005_uv.MS \ /var/lib/cwl/stg55dc76f5-ce12-462c-bffd-1f6d2e4d66bb/L755125_SB004_uv.MS \ /var/lib/cwl/stgf8d851aa-9737-4120-af95-241e53ef984b/L755125_SB006_uv.MS \ /var/lib/cwl/stg2d1ebe28-a26f-4442-a4f7-e9fb177653fe/L755125_SB007_uv.MS \ /var/lib/cwl/stgf4f9f1b2-855c-433f-87fc-f9b57e69f060/L755125_SB013_uv.MS \ /var/lib/cwl/stgfbef4e7b-b90e-49eb-bb24-bc9074dec3ef/L755125_SB010_uv.MS \ [...] --min_separation \ 30 \ --outputimage \ Ateam_separation.png > /project/astroneosc/Data/tmp/node-70e26f65-197b-49f9-90aa-52b42e8d7822-4b184c8e-e9fd-4784-92c4-5ace3fd7ef2c/tmp074diqpq/31cdf995-536c-4d07-9b48-c72e6 df42315/tu3w97mbq/tmp-outcd3vx2cf/Ateam_separation.log [2020-12-02T11:21:43+0100] [MainThread] [E] [cwltool] Exception while running job Traceback (most recent call last): File "/home/astroneosc-mmancini/.local/lib/python3.6/site-packages/cwltool/job.py", line 394, in _execute default_stderr=runtimeContext.default_stderr, File "/home/astroneosc-mmancini/.local/lib/python3.6/site-packages/cwltool/job.py", line 955, in _job_popen universal_newlines=True, File "/usr/lib64/python3.6/subprocess.py", line 729, in __init__ restore_signals, start_new_session) File "/usr/lib64/python3.6/subprocess.py", line 1364, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) OSError: [Errno 7] Argument list too long: 'singularity' [2020-12-02T11:21:43+0100] [MainThread] [W] [cwltool] [job check_ateam_separation] completed permanentFail [2020-12-02T11:21:45+0100] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-MASTER: Job used more disk than requested. Consider modifying the user script to avoid th e chance of failure due to incorrectly requested resources. Job files/for-job/kind-CWLWorkflow/instance-rcfqyxlv/cleanup/file-5wk8511s/stream used 2725.25% (81.8 GB [87786401792B] used , 3.0 GB [3221225472B] requested) at the end of its run. Traceback (most recent call last): File "/home/astroneosc-mmancini/.local/lib/python3.6/site-packages/toil/worker.py", line 368, in workerScript job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/home/astroneosc-mmancini/.local/lib/python3.6/site-packages/toil/job.py", line 1424, in _runner returnValues = self._run(jobGraph, fileStore) File "/home/astroneosc-mmancini/.local/lib/python3.6/site-packages/toil/job.py", line 1361, in _run return self.run(fileStore) File "/home/astroneosc-mmancini/.local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 988, in run raise cwltool.errors.WorkflowException(status) cwltool.errors.WorkflowException: permanentFail [2020-12-02T11:21:45+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-db-02.novalocal ``` I redacted out the boring stuff ---
**Author:** ![mrc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/mrc/32/3_2.png) [@mrc](https://cwl.discourse.group/u/mrc)\ **Post date:** [December 2, 2020, 10:51am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/5 "2020-12-02T10:51:31Z")
Looks like the loop in [https://github.com/common-workflow-language/cwltool/blob/78fe9d41ee5a44f8725dfbd7028e4a5ee42949cf/cwltool/job.py#L685](https://github.com/common-workflow-language/cwltool/blob/78fe9d41ee5a44f8725dfbd7028e4a5ee42949cf/cwltool/job.py#L685) is responsible as it doesn’t check to see if the File or Directory is part of a Directory that has already been added. A possible workaround might be to change the `cwlVersion: v1.0` to `cwlVersion: v1.1` as we default to not enumerating the contents of `Directory` classes, unless requested: [https://www.commonwl.org/v1.1/CommandLineTool.html#Changelog](https://www.commonwl.org/v1.1/CommandLineTool.html#Changelog) ---
**Author:** ![matmanc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/matmanc/32/113_2.png) [@matmanc](https://cwl.discourse.group/u/matmanc)\ **Post date:** [December 2, 2020, 10:54am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/6 "2020-12-02T10:54:20Z")
Should I change all the cwl files including the workflow or only this specific step? ---
**Author:** ![mrc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/mrc/32/3_2.png) [@mrc](https://cwl.discourse.group/u/mrc)\ **Post date:** [December 2, 2020, 10:59am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/7 "2020-12-02T10:59:26Z")
Just that step. What version of Toil are you using? ---
**Author:** ![matmanc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/matmanc/32/113_2.png) [@matmanc](https://cwl.discourse.group/u/matmanc)\ **Post date:** [December 2, 2020, 11:00am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/8 "2020-12-02T11:00:11Z")
So the version I am using is the: 4.2.0 ---
**Author:** ![mrc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/mrc/32/3_2.png) [@mrc](https://cwl.discourse.group/u/mrc)\ **Post date:** [December 2, 2020, 11:03am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/9 "2020-12-02T11:03:44Z")
That version of Toil shouldn’t have a problem with `cwlVersion: v1.1` as it is the latest version: [https://pypi.org/project/toil/](https://pypi.org/project/toil/) I hope it works! ---
**Author:** ![matmanc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/matmanc/32/113_2.png) [@matmanc](https://cwl.discourse.group/u/matmanc)\ **Post date:** [December 2, 2020, 11:05am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/10 "2020-12-02T11:05:00Z")
In case it doesnt is there a way to work around the issue? Maybe an InputWorkDirRequirement? ---
**Author:** ![matmanc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/matmanc/32/113_2.png) [@matmanc](https://cwl.discourse.group/u/matmanc)\ **Post date:** [December 2, 2020, 11:22am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/11 "2020-12-02T11:22:27Z")
So, it seems that the problem persists even though I changed it to a version 1.1. Can it be caused by some GatherStep? ---
**Author:** ![matmanc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/matmanc/32/113_2.png) [@matmanc](https://cwl.discourse.group/u/matmanc)\ **Post date:** [December 2, 2020, 11:25am UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/12 "2020-12-02T11:25:14Z")
Here is the log ``` 01+0100] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'file:///project/astroneosc/Software/prefactor3-cwl/lofar-cwl/steps /check_ateam_separation.cwl#check_ateam_separation' python3 /usr/local/bin/check_Ateam_separation.py kind-file_project_astroneosc_Software_prefactor3-cwl_lofar-cwl_steps_check_ateam_se paration.cwl_check_ateam_separation/instance-twjhltat [2020-12-02T12:23:01+0100] [MainThread] [W] [toil.leader] Log from job kind-file_project_astroneosc_Software_prefactor3-cwl_lofar-cwl_steps_check_ateam_separation.cwl_check_ateam_separ ation/instance-twjhltat follows: =========> /table.dat:ro \ --bind \ /project/astroneosc/Data/tmp/node-dd6b59bf-01ca-44f4-8c4f-f1c40c45ab7e-b7562762-34ca-4a24-bcdd-d6a811d0201b/tmp6udp2o3w/5dc3e6bd-9858-40e2-9f6d-4a34086a7c90/tmpo4m7rlpd.tmp :/var/lib/cwl/stg4615cab6-2798-45b4-9f0c-ab3bb9f64241/L755125_SB222_uv.MS/table.f4_TSM0:ro \ --bind \ /project/astroneosc/Data/tmp/node-dd6b59bf-01ca-44f4-8c4f-f1c40c45ab7e-b7562762-34ca-4a24-bcdd-d6a811d0201b/tmp6udp2o3w/5dc3e6bd-9858-40e2-9f6d-4a34086a7c90/tmpq7kwy461.tmp :/var/lib/cwl/stg4615cab6-2798-45b4-9f0c-ab3bb9f64241/L755125_SB222_uv.MS/DATA_DESCRIPTION/table.info:ro \ --bind \ /project/astroneosc/Data/tmp/node-dd6b59bf-01ca-44f4-8c4f-f1c40c45ab7e-b7562762-34ca-4a24-bcdd-d6a811d0201b/tmp6udp2o3w/5dc3e6bd-9858-40e2-9f6d-4a34086a7c90/tmppc2l734s.tmp :/var/lib/cwl/stg4615cab6-2798-45b4-9f0c-ab3bb9f64241/L755125_SB222_uv.MS/DATA_DESCRIPTION/table.f0:ro \ --bind \ /project/astroneosc/Data/tmp/node-dd6b59bf-01ca-44f4-8c4f-f1c40c45ab7e-b7562762-34ca-4a24-bcdd-d6a811d0201b/tmp6udp2o3w/5dc3e6bd-9858-40e2-9f6d-4a34086a7c90/tmpfq7oakbk.tmp :/var/lib/cwl/stg4615cab6-2798-45b4-9f0c-ab3bb9f64241/L755125_SB222_uv.MS/DATA_DESCRIPTION/table.dat:ro \ --bind \ /project/astroneosc/Data/tmp/node-dd6b59bf-01ca-44f4-8c4f-f1c40c45ab7e-b7562762-34ca-4a24-bcdd-d6a811d0201b/tmp6udp2o3w/5dc3e6bd-9858-40e2-9f6d-4a34086a7c90/tmpz184dsvg.tmp :/var/lib/cwl/stg4615cab6-2798-45b4-9f0c-ab3bb9f64241/L755125_SB222_uv.MS/table.f0:ro \ --bind \ /project/astroneosc/Data/tmp/node-dd6b59bf-01ca-44f4-8c4f-f1c40c45ab7e-b7562762-34ca-4a24-bcdd-d6a811d0201b/tmp6udp2o3w/5dc3e6bd-9858-40e2-9f6d-4a34086a7c90/tmp5qv654ri.tmp :/var/lib/cwl/stg4615cab6-2798-45b4-9f0c-ab3bb9f64241/L755125_SB222_uv.MS/QUALITY_FREQUENCY_STATISTIC/table.info:ro \ --bind \ /project/astroneosc/Data/tmp/node-dd6b59bf-01ca-44f4-8c4f-f1c40c45ab7e-b7562762-34ca-4a24-bcdd-d6a811d0201b/tmp6udp2o3w/5dc3e6bd-9858-40e2-9f6d-4a34086a7c90/tmpbctexdj6.tmp :/var/lib/cwl/stg4615cab6-2798-45b4-9f0c-ab3bb9f64241/L755125_SB222_uv.MS/QUALITY_FREQUENCY_STATISTIC/table.f0:ro \ [...] --pwd \ /DxeKMf \ /project/astroneosc/Software/prefactor3.simg \ python3 \ /usr/local/bin/check_Ateam_separation.py \ /var/lib/cwl/stg15b2528c-1b4a-4f9f-a7a3-bf8e43d389b9/L755125_SB000_uv.MS \ /var/lib/cwl/stg409537df-ebbe-4ae3-bb80-0c13caba3302/L755125_SB002_uv.MS \ /var/lib/cwl/stgbb834c53-5f1e-4197-8714-fd207a152788/L755125_SB005_uv.MS \ /var/lib/cwl/stgadad000d-0856-4b13-b956-d14fa22404e1/L755125_SB004_uv.MS \ /var/lib/cwl/stg842b4160-f25d-4ba3-942d-cd77fb7a71e4/L755125_SB006_uv.MS \ /var/lib/cwl/stg3bc51532-d697-4acc-8350-a04e03d22bfb/L755125_SB007_uv.MS \ /var/lib/cwl/stg5668b9bb-177b-4dcc-a626-d7ea33b4f22e/L755125_SB013_uv.MS \ /var/lib/cwl/stg46adea18-2eaa-4a67-8ad7-26b0adcda346/L755125_SB010_uv.MS \ /var/lib/cwl/stg25502d25-4aff-4a21-976d-e8abc18dc865/L755125_SB011_uv.MS \ /var/lib/cwl/stg67986c8f-e1b3-4c5c-9d0b-9384fcd6d609/L755125_SB008_uv.MS \ [...] --min_separation \ 30 \ --outputimage \ Ateam_separation.png > /project/astroneosc/Data/tmp/node-dd6b59bf-01ca-44f4-8c4f-f1c40c45ab7e-b7562762-34ca-4a24-bcdd-d6a811d0201b/tmp6udp2o3w/5dc3e6bd-9858-40e2-9f6d-4a340 86a7c90/tb1hlymy6/tmp-outt7xt8yfi/Ateam_separation.log [2020-12-02T12:22:57+0100] [MainThread] [E] [cwltool] Exception while running job Traceback (most recent call last): File "/home/astroneosc-mmancini/.local/lib/python3.6/site-packages/cwltool/job.py", line 394, in _execute default_stderr=runtimeContext.default_stderr, File "/home/astroneosc-mmancini/.local/lib/python3.6/site-packages/cwltool/job.py", line 955, in _job_popen universal_newlines=True, File "/usr/lib64/python3.6/subprocess.py", line 729, in __init__ restore_signals, start_new_session) File "/usr/lib64/python3.6/subprocess.py", line 1364, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) OSError: [Errno 7] Argument list too long: 'singularity' [2020-12-02T12:22:57+0100] [MainThread] [W] [cwltool] [job check_ateam_separation] completed permanentFail [2020-12-02T12:22:57+0100] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-MASTER: Job used more disk than requested. Consider modifying the user script to avoid th e chance of failure due to incorrectly requested resources. Job files/for-job/kind-CWLWorkflow/instance-zznwcosd/cleanup/file-cauu9w_p/stream used 2725.25% (81.8 GB [87786401792B] used , 3.0 GB [3221225472B] requested) at the end of its run. Traceback (most recent call last): File "/home/astroneosc-mmancini/.local/lib/python3.6/site-packages/toil/worker.py", line 368, in workerScript job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) File "/home/astroneosc-mmancini/.local/lib/python3.6/site-packages/toil/job.py", line 1424, in _runner returnValues = self._run(jobGraph, fileStore) File "/home/astroneosc-mmancini/.local/lib/python3.6/site-packages/toil/job.py", line 1361, in _run return self.run(fileStore) File "/home/astroneosc-mmancini/.local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 988, in run raise cwltool.errors.WorkflowException(status) cwltool.errors.WorkflowException: permanentFail [2020-12-02T12:22:57+0100] [MainThread] [E] [toil.worker] Exiting the worker because of a ``` failed job on host wn-db-03.novalocal ---
**Author:** ![mrc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/mrc/32/3_2.png) [@mrc](https://cwl.discourse.group/u/mrc)\ **Post date:** [December 3, 2020, 4:05pm UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/14 "2020-12-03T16:05:39Z")
That’s cool, I didn’t know about `SINGULARITY_BIND`; yeah, that would probably work ---
**Author:** ![matmanc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/matmanc/32/113_2.png) [@matmanc](https://cwl.discourse.group/u/matmanc)\ **Post date:** [December 3, 2020, 5:24pm UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/15 "2020-12-03T17:24:50Z")
I tried to change cwltool but something goes wrong anyway with the same error. I am really confused 😕 I am trying now to create an CommandLineTool that copies everything in one directory and then it just passed that one. But I dont know if that would work either. After that I am out of ideas. Do you have any? ---
**Author:** ![tetron](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/tetron/32/40_2.png) [@tetron](https://cwl.discourse.group/u/tetron)\ **Post date:** [December 3, 2020, 8:56pm UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/16 "2020-12-03T20:56:09Z")
Try changing everything (workflow and tools) to `cwlVersion: v1.1` and then try it with `cwltool` again. ---
**Author:** ![matmanc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/matmanc/32/113_2.png) [@matmanc](https://cwl.discourse.group/u/matmanc)\ **Post date:** [December 3, 2020, 9:21pm UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/17 "2020-12-03T21:21:15Z")
I will try to make a small example that fails tomorrow than I will post it here. I tried already to convert everything in v1.1 but it didnt work. ---
**Author:** ![tetron](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/tetron/32/40_2.png) [@tetron](https://cwl.discourse.group/u/tetron)\ **Post date:** [December 3, 2020, 10:46pm UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/18 "2020-12-03T22:46:44Z")
Does `toil` have an explicit notion of directories in its file store abstraction, or is it still up to `toil-cwl-runner` to enumerate directory contents? Some method of passing a list of binds to singularity that isn’t constrained by command line limits would be a good solution. ---
**Author:** ![matmanc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/matmanc/32/113_2.png) [@matmanc](https://cwl.discourse.group/u/matmanc)\ **Post date:** [December 4, 2020, 12:01pm UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/19 "2020-12-04T12:01:34Z")
I have the fear that that is the case. In fact the jobstore is created with a bunch of single files in a nested directory structure. There is the SINGULARITY\_BIND env variable that you can set to do that. But when I tried to change the singularity.py module in cwltool I still get the error. I have a feeling that the env variable and the command are executed on the same line. Do you know what file I should be looking at ? Do you know if using the InputWorkDirRequirement would solve the issue? ---
**Author:** ![matmanc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/matmanc/32/113_2.png) [@matmanc](https://cwl.discourse.group/u/matmanc)\ **Post date:** [December 4, 2020, 2:50pm UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/20 "2020-12-04T14:50:04Z")
create\_files.cwl ``` class: CommandLineTool cwlVersion: v1.1 $namespaces: sbg: 'https://www.sevenbridges.com/' id: create_files_cwl baseCommand: - bash inputs: [] outputs: - id: output type: 'Directory[]' outputBinding: glob: out/* label: create_files.cwl arguments: - prefix: '' shellQuote: false position: 0 valueFrom: script.sh requirements: - class: ShellCommandRequirement - class: InitialWorkDirRequirement listing: - entryname: script.sh entry: |- #!/bin/bash for i in {1..2024} do for k in {1..20} do mkdir -p out/$i/$k/ for s in {1..30} do touch out/$i/$k/$s done done done writable: false ``` find.cwl ``` class: CommandLineTool cwlVersion: v1.1 id: find baseCommand: - ls inputs: - id: input type: 'Directory[]' inputBinding: shellQuote: false position: 0 outputs: - id: output type: File? outputBinding: glob: stout label: find requirements: - class: ShellCommandRequirement - class: DockerRequirement dockerPull: 'ubuntu:latest' stdout: stout ``` test\_too\_many\_files\_workflow.cwl ``` class: Workflow cwlVersion: v1.0 id: test_too_many_arguments label: test_too_many_arguments inputs: [] outputs: - id: output outputSource: - find/output type: File? steps: - id: find in: - id: input source: - create_files_cwl/output out: - id: output run: ./find.cwl label: find - id: create_files_cwl in: [] out: - id: output run: ./create_files.cwl label: create_files.cwl requirements: - class: InlineJavascriptRequirement - class: StepInputExpressionRequirement ``` ---
**Author:** ![tetron](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/tetron/32/40_2.png) [@tetron](https://cwl.discourse.group/u/tetron)\ **Post date:** [December 4, 2020, 3:02pm UTC](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/21 "2020-12-04T15:02:20Z")
So I think the problem is that the `toil` file store only handles single files, not directories. The CWL layer makes up for this by enumerating the files itself, and reconstructing the directory structure when it is time to run a tool. The way it reconstructs the directory is either by making a bunch of symlinks (when not running inside a container) or by setting up bind mounts (when using containers). Unfortunately it is with that second approach that you are running into scaling issues. > [@matmanc](#): > > In case it doesnt is there a way to work around the issue? > Maybe an InputWorkDirRequirement? The InitialWorkDirRequirement uses the same strategies so I don’t think it will work. Ideas for solutions (need to fix in `cwltool` and then update `toil`): - Some way of invoking singularity with an arbitrary number of binds - Construct the directory structure outside the container by copying the files, then bind mount only the directory - Construct the directory structure outside the container by hardlinking the files, then bind mount only the directory - Construct the directory structure outside the container by bind mounting the file store into the container so that symlinks are valid Unfortunately I don’t have a good workaround on the user side, except for trying a different runner. For example, `cwltool` handles Directories differently than `toil` that might scale better. [Next page](https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248.md?page=2)