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Galaxy Workflows maintained by the Intergalactic Workflow Commission
https://dockstore.org/organizations/iwc
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Updating workflows/amplicon/qiime2/qiime2-I-import from 0.2 to 0.3 #422

Open gxydevbot opened 3 months ago

gxydevbot commented 3 months ago

Hello! This is an automated update of the following workflow: workflows/amplicon/qiime2/qiime2-I-import. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

The workflow release number has been updated from 0.2 to 0.3.

The workflow release number has been updated from 0.2 to 0.3.

bernt-matthias commented 3 months ago

@mvdbeek could you point me to the logs where it shows the reason for not updating?

I tried locally: if I run the autoupdate 2x then c is updated...

lldelisle commented 3 months ago

I got the same bug with #429 all 3 workflows of the directory should have been updated...

github-actions[bot] commented 3 months ago

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 4
Passed 3
Error 1
Failure 0
Skipped 0
Errored Tests *
❌ QIIME2-Id-demultiplexed-data-paired-end.ga_0
**Execution Problem:** * ``` Failed to run workflow, at least one job is in [error] state. ``` #### Workflow invocation details * Invocation Messages *
Steps - **Step 1: Sequence collection**: * step_state: scheduled - **Step 2: Extract element identifiers**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console mv '/tmp/tmpo3e9ek65/job_working_directory/000/30/configs/tmpx0_uzjy0' '/tmp/tmpo3e9ek65/job_working_directory/000/30/outputs/dataset_b19671e3-6c99-4267-8271-77f6da64b715.dat' ``` **Exit Code:** * ```console 0 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "fastqsanger.gz" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "e55208ec26e311ef89a8e76d21b9ab60" ` | | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | input\_collection | ` {"values": [{"id": 3, "src": "hdca"}]} ` | 
 - **Step 3: Screening laneless and single-lane**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/tmp/tmpo3e9ek65/files/b/1/9/dataset_b19671e3-6c99-4267-8271-77f6da64b715.dat' --output '/tmp/tmpo3e9ek65/job_working_directory/000/31/outputs/dataset_e5679c72-6c64-4fcc-abc4-614ff014c049.dat' --input_display_name 'Extract element identifiers on data 6, data 5, and others' --pattern='_L[0-9][0-9][0-9]_' --replacement='_'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "e55208ec26e311ef89a8e76d21b9ab60" ` |
             | checks | ` [{"__index__": 0, "pattern": "_L[0-9][0-9][0-9]_", "replacement": "_"}] ` |
             | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |

      </details>

 - **Step 4: Relabel sequence files**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "e55208ec26e311ef89a8e76d21b9ab60" ` |
             | how | ` {"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 35, "src": "hda"}]}, "strict": false} ` |
             | input | ` {"values": [{"id": 3, "src": "hdca"}]} ` |

      </details>

 - **Step 5: Import data into the pipeline**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is error

        **Command Line:**

         * ```console
           q2galaxy run tools import '/tmp/tmpo3e9ek65/job_working_directory/000/33/configs/tmpjjwykbnu'
           ```
        **Exit Code:**

         * ```console
           125
           ```
        **Standard Error:**

         * ```console
           Unable to find image 'quay.io/qiime2/core:2023.5' locally
           2023.5: Pulling from qiime2/core
           42c077c10790: Pulling fs layer
           1a23c9d790a3: Pulling fs layer
           22a6fc63b9b5: Pulling fs layer
           dd499ae3733f: Pulling fs layer
           012a2b6b385e: Pulling fs layer
           dd499ae3733f: Waiting
           012a2b6b385e: Waiting
           0921518aca19: Pulling fs layer
           1c0e12e18f94: Pulling fs layer
           0921518aca19: Waiting
           1413bc183df8: Pulling fs layer
           1c0e12e18f94: Waiting
           795207d4f19b: Pulling fs layer
           96364662752a: Pulling fs layer
           c3edffcb7ece: Pulling fs layer
           1413bc183df8: Waiting
           795207d4f19b: Waiting
           96364662752a: Waiting
           3f541efa0329: Pulling fs layer
           8ebefce780ee: Pulling fs layer
           ee2b99347e51: Pulling fs layer
           c6e473dc65aa: Pulling fs layer
           c3edffcb7ece: Waiting
           3f541efa0329: Waiting
           8ebefce780ee: Waiting
           ee2b99347e51: Waiting
           c6e473dc65aa: Waiting
           42c077c10790: Verifying Checksum
           42c077c10790: Download complete
           dd499ae3733f: Verifying Checksum
           dd499ae3733f: Download complete
           1a23c9d790a3: Verifying Checksum
           1a23c9d790a3: Download complete
           22a6fc63b9b5: Verifying Checksum
           22a6fc63b9b5: Download complete
           0921518aca19: Verifying Checksum
           0921518aca19: Download complete
           1c0e12e18f94: Verifying Checksum
           1c0e12e18f94: Download complete
           1413bc183df8: Verifying Checksum
           1413bc183df8: Download complete
           96364662752a: Verifying Checksum
           96364662752a: Download complete
           c3edffcb7ece: Verifying Checksum
           c3edffcb7ece: Download complete
           3f541efa0329: Verifying Checksum
           3f541efa0329: Download complete
           8ebefce780ee: Verifying Checksum
           8ebefce780ee: Download complete
           012a2b6b385e: Verifying Checksum
           012a2b6b385e: Download complete
           ee2b99347e51: Verifying Checksum
           ee2b99347e51: Download complete
           c6e473dc65aa: Verifying Checksum
           c6e473dc65aa: Download complete
           42c077c10790: Pull complete
           1a23c9d790a3: Pull complete
           22a6fc63b9b5: Pull complete
           dd499ae3733f: Pull complete
           795207d4f19b: Verifying Checksum
           795207d4f19b: Download complete
           012a2b6b385e: Pull complete
           0921518aca19: Pull complete
           1c0e12e18f94: Pull complete
           1413bc183df8: Pull complete
           docker: failed to register layer: write /opt/conda/envs/qiime2-2023.5/libexec/gcc/x86_64-conda-linux-gnu/12.2.0/cc1: no space left on device.
           See 'docker run --help'.

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "e55208ec26e311ef89a8e76d21b9ab60" ` |
             | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |
             | import\_root | ` {"__current_case__": 46, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "CasavaOneEightLanelessPerSampleDirFmt", "import_sequences": {"__q2galaxy__GUI__cond__sequences__": {"__current_case__": 0, "__q2galaxy__GUI__cond__add_ext__": {"__current_case__": 1, "__q2galaxy__GUI__select__ext_pick__": "no"}, "__q2galaxy__GUI__select__picker__": "collection", "elements": {"values": [{"id": 4, "src": "hdca"}]}}}}, "type": "SampleData__ob__PairedEndSequencesWithQuality__cb__"} ` |

      </details>

 - **Step 6: Summarising the demultiplexed output**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is paused

        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"n": "10000"} ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "e55208ec26e311ef89a8e76d21b9ab60" ` |
             | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |

      </details>
  </details>
  • Other invocation details - **error_message** * Failed to run workflow, at least one job is in [error] state. - **history_id** * 669901bb54198fac - **history_state** * error - **invocation_id** * 669901bb54198fac - **invocation_state** * scheduled - **workflow_id** * 669901bb54198fac

Passed Tests *
✅ QIIME2-Ia-multiplexed-data-single-end.ga_0
#### Workflow invocation details * Invocation Messages *
Steps - **Step 1: Sequences**: * step_state: scheduled - **Step 2: Barcodes**: * step_state: scheduled - **Step 3: Metadata**: * step_state: scheduled - **Step 4: Metadata parameter**: * step_state: scheduled - **Step 5: Reverse complement barcodes**: * step_state: scheduled - **Step 6: Input files**: * step_state: scheduled *
Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run tools import '/tmp/tmpo3e9ek65/job_working_directory/000/4/configs/tmpcumx63x1' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢type: EMPSingleEndSequences｣ ｢format: EMPSingleEndDirFmt｣ ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "abf73f9226e111ef89a8e76d21b9ab60" ` | | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | import\_root | ` {"__current_case__": 7, "__q2galaxy__GUI__cond__format__": {"__current_case__": 1, "format": "EMPSingleEndDirFmt", "import_barcodes": {"data": {"values": [{"id": 2, "src": "hda"}]}, "name": "barcodes.fastq.gz"}, "import_sequences": {"data": {"values": [{"id": 1, "src": "hda"}]}, "name": "sequences.fastq.gz"}}, "type": "EMPSingleEndSequences"} ` | 
 - **Step 7: Metadata as artifact**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           q2galaxy run tools import '/tmp/tmpo3e9ek65/job_working_directory/000/5/configs/tmppyvky0y8'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Output:**

         * ```console
           ｢type: ImmutableMetadata｣
           ｢format: ImmutableMetadataFormat｣

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "abf73f9226e111ef89a8e76d21b9ab60" ` |
             | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |
             | import\_root | ` {"__current_case__": 48, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 3, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"} ` |

      </details>

 - **Step 8: Demultiplex single-end data**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           q2galaxy run demux emp_single '/tmp/tmpo3e9ek65/job_working_directory/000/6/configs/tmp53selfg8'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Output:**

         * ```console
           ｢seqs: 27388997-cb18-47ef-92b9-ce152a4bac8a｣
           ｢barcodes: <CategoricalMetadataColumn name='barcode-sequence' id_count=34>｣
           ｢golay_error_correction: True｣
           ｢rev_comp_barcodes: False｣
           ｢rev_comp_mapping_barcodes: False｣
           ｢ignore_description_mismatch: False｣

           Saved SampleData[SequencesWithQuality] to: per_sample_sequences.qza
           Saved ErrorCorrectionDetails to: error_correction_details.qza

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"golay_error_correction": true, "ignore_description_mismatch": false, "rev_comp_barcodes": false, "rev_comp_mapping_barcodes": false} ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "abf73f9226e111ef89a8e76d21b9ab60" ` |
             | barcodes | ` {"__current_case__": 1, "column": "barcode-sequence", "source": {"values": [{"id": 5, "src": "hda"}]}, "type": "qza"} ` |
             | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |

      </details>

 - **Step 9: Summarize demultiplexed output**:

    * step_state: scheduled

    * <details><summary>Jobs</summary>

      - **Job 1:**

        * Job state is ok

        **Command Line:**

         * ```console
           q2galaxy run demux summarize '/tmp/tmpo3e9ek65/job_working_directory/000/7/configs/tmp6km6zgdo'
           ```
        **Exit Code:**

         * ```console
           0
           ```
        **Standard Error:**

         * ```console
           /opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/seaborn/_oldcore.py:1119: FutureWarning: use_inf_as_na option is deprecated and will be removed in a future version. Convert inf values to NaN before operating instead.
             with pd.option_context('mode.use_inf_as_na', True):
           /opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_demux/_summarize/_visualizer.py:180: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.
             context['result_data'] = pd.concat([context['result_data'], df])
           /opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_demux/_summarize/_visualizer.py:74: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '['152 nts' '152 nts' '152 nts' '152 nts' '152 nts' '152 nts' '152 nts']' has dtype incompatible with float64, please explicitly cast to a compatible dtype first.
             stats[stats.index != 'count'] = \

           ```
        **Standard Output:**

         * ```console
           ｢data: 2b1b85ab-1e26-41bf-b378-2505bac0a6f6｣
           ｢n: 10000｣

           Saved Visualization to: visualization.qzv

           ```
        **Traceback:**

         * ```console

           ```
        **Job Parameters:**

         *   | Job parameter | Parameter value |
             | ------------- | --------------- |
             | \_\_input\_ext | ` "input" ` |
             | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"n": "10000"} ` |
             | \_\_workflow\_invocation\_uuid\_\_ | ` "abf73f9226e111ef89a8e76d21b9ab60" ` |
             | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` |
             | dbkey | ` "?" ` |

      </details>
  </details>
  • Other invocation details - **history_id** * 91ad1f11f95a32d4 - **history_state** * ok - **invocation_id** * 91ad1f11f95a32d4 - **invocation_state** * scheduled - **workflow_id** * 91ad1f11f95a32d4

  • ✅ QIIME2-Ib-multiplexed-data-paired-end.ga_0
    #### Workflow invocation details * Invocation Messages *
    Steps - **Step 1: Forward sequences**: * step_state: scheduled - **Step 2: Reverse sequences**: * step_state: scheduled - **Step 3: Barcodes**: * step_state: scheduled - **Step 4: Metadata**: * step_state: scheduled - **Step 5: Metadata parameter**: * step_state: scheduled - **Step 6: Reverse complement of barcodes needed?**: * step_state: scheduled - **Step 7: Import data into the pipeline**: * step_state: scheduled *
    Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run tools import '/tmp/tmpo3e9ek65/job_working_directory/000/12/configs/tmpmqg6ywd9' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢type: EMPPairedEndSequences｣ ｢format: EMPPairedEndDirFmt｣ ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "5908059026e211ef89a8e76d21b9ab60" ` | | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | import\_root | ` {"__current_case__": 6, "__q2galaxy__GUI__cond__format__": {"__current_case__": 1, "format": "EMPPairedEndDirFmt", "import_barcodes": {"data": {"values": [{"id": 11, "src": "hda"}]}, "name": "barcodes.fastq.gz"}, "import_forward": {"data": {"values": [{"id": 9, "src": "hda"}]}, "name": "forward.fastq.gz"}, "import_reverse": {"data": {"values": [{"id": 10, "src": "hda"}]}, "name": "reverse.fastq.gz"}}, "type": "EMPPairedEndSequences"} ` |

    • Step 8: Metadata as artifact:

      • step_state: scheduled

      • Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run tools import '/tmp/tmpo3e9ek65/job_working_directory/000/13/configs/tmpzduuxm2u' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢type: ImmutableMetadata｣ ｢format: ImmutableMetadataFormat｣ ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "5908059026e211ef89a8e76d21b9ab60" ` | | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | import\_root | ` {"__current_case__": 48, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "ImmutableMetadataFormat", "import": {"data": {"values": [{"id": 12, "src": "hda"}]}, "name": "__q2galaxy__::literal::None"}}, "type": "ImmutableMetadata"} ` |

    • Step 9: Demultiplex paired-end sequences:

      • step_state: scheduled

      • Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run demux emp_paired '/tmp/tmpo3e9ek65/job_working_directory/000/14/configs/tmp3chv84xx' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢seqs: 943a7465-e3c3-4ed3-8037-66b9b14e8d80｣ ｢barcodes: ｣ ｢golay_error_correction: True｣ ｢rev_comp_barcodes: False｣ ｢rev_comp_mapping_barcodes: True｣ ｢ignore_description_mismatch: False｣ Saved SampleData[PairedEndSequencesWithQuality] to: per_sample_sequences.qza Saved ErrorCorrectionDetails to: error_correction_details.qza ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"golay_error_correction": true, "ignore_description_mismatch": false, "rev_comp_barcodes": false, "rev_comp_mapping_barcodes": true} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "5908059026e211ef89a8e76d21b9ab60" ` | | barcodes | ` {"__current_case__": 1, "column": "barcode-sequence", "source": {"values": [{"id": 14, "src": "hda"}]}, "type": "qza"} ` | | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` |

    • Step 10: Summarising the demultiplexed output:

      • step_state: scheduled

      • Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run demux summarize '/tmp/tmpo3e9ek65/job_working_directory/000/15/configs/tmp7py2w_no' ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/seaborn/_oldcore.py:1119: FutureWarning: use_inf_as_na option is deprecated and will be removed in a future version. Convert inf values to NaN before operating instead. with pd.option_context('mode.use_inf_as_na', True): /opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_demux/_summarize/_visualizer.py:180: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. context['result_data'] = pd.concat([context['result_data'], df]) /opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_demux/_summarize/_visualizer.py:74: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '['151 nts' '151 nts' '151 nts' '151 nts' '151 nts' '151 nts' '151 nts']' has dtype incompatible with float64, please explicitly cast to a compatible dtype first. stats[stats.index != 'count'] = \ /opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/seaborn/_oldcore.py:1119: FutureWarning: use_inf_as_na option is deprecated and will be removed in a future version. Convert inf values to NaN before operating instead. with pd.option_context('mode.use_inf_as_na', True): /opt/conda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_demux/_summarize/_visualizer.py:74: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '['151 nts' '151 nts' '151 nts' '151 nts' '151 nts' '151 nts' '151 nts']' has dtype incompatible with float64, please explicitly cast to a compatible dtype first. stats[stats.index != 'count'] = \ ``` **Standard Output:** * ```console ｢data: 88538a00-7b71-4f0f-adc5-6af6dd082bba｣ ｢n: 10000｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"n": "10000"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "5908059026e211ef89a8e76d21b9ab60" ` | | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` |

  • Other invocation details - **history_id** * ab92eaf80407a21f - **history_state** * ok - **invocation_id** * ab92eaf80407a21f - **invocation_state** * scheduled - **workflow_id** * ab92eaf80407a21f

  • ✅ QIIME2-Ic-demultiplexed-data-single-end.ga_0
    #### Workflow invocation details * Invocation Messages *
    Steps - **Step 1: Sequence collection**: * step_state: scheduled - **Step 2: Extract element identifiers**: * step_state: scheduled *
    Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console mv '/tmp/tmpo3e9ek65/job_working_directory/000/19/configs/tmpzjygeyiv' '/tmp/tmpo3e9ek65/job_working_directory/000/19/outputs/dataset_6fb29116-748f-4c3d-af44-85f0f64ff7bc.dat' ``` **Exit Code:** * ```console 0 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "fastqsanger.gz" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "066906bc26e311ef89a8e76d21b9ab60" ` | | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | input\_collection | ` {"values": [{"id": 1, "src": "hdca"}]} ` |

    • Step 3: Screening laneless and single-lane:

      • step_state: scheduled

      • Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/tmp/tmpo3e9ek65/files/6/f/b/dataset_6fb29116-748f-4c3d-af44-85f0f64ff7bc.dat' --output '/tmp/tmpo3e9ek65/job_working_directory/000/20/outputs/dataset_4cfb1f30-6159-448d-9d86-8d27b4f35146.dat' --input_display_name 'Extract element identifiers on data 3, data 2, and data 1' --pattern='_L[0-9][0-9][0-9]_' --replacement='_' ``` **Exit Code:** * ```console 0 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "066906bc26e311ef89a8e76d21b9ab60" ` | | checks | ` [{"__index__": 0, "pattern": "_L[0-9][0-9][0-9]_", "replacement": "_"}] ` | | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` |

    • Step 4: Relabel sequence files:

      • step_state: scheduled

      • Jobs - **Job 1:** * Job state is ok **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_workflow\_invocation\_uuid\_\_ | ` "066906bc26e311ef89a8e76d21b9ab60" ` | | how | ` {"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 22, "src": "hda"}]}, "strict": false} ` | | input | ` {"values": [{"id": 1, "src": "hdca"}]} ` |

    • Step 5: Import data into the pipeline:

      • step_state: scheduled

      • Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run tools import '/tmp/tmpo3e9ek65/job_working_directory/000/22/configs/tmps0dm3bfi' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢type: SampleData[SequencesWithQuality]｣ ｢format: CasavaOneEightLanelessPerSampleDirFmt｣ ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "066906bc26e311ef89a8e76d21b9ab60" ` | | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` | | import\_root | ` {"__current_case__": 63, "__q2galaxy__GUI__cond__format__": {"__current_case__": 0, "format": "CasavaOneEightLanelessPerSampleDirFmt", "import_sequences": {"__q2galaxy__GUI__cond__sequences__": {"__current_case__": 0, "__q2galaxy__GUI__cond__add_ext__": {"__current_case__": 1, "__q2galaxy__GUI__select__ext_pick__": "no"}, "__q2galaxy__GUI__select__picker__": "collection", "elements": {"values": [{"id": 2, "src": "hdca"}]}}}}, "type": "SampleData__ob__SequencesWithQuality__cb__"} ` |

    • Step 6: Summarising the demultiplexed output:

      • step_state: scheduled

      • Jobs - **Job 1:** * Job state is ok **Command Line:** * ```console q2galaxy run demux summarize '/tmp/tmpo3e9ek65/job_working_directory/000/23/configs/tmpo4mfv_o_' ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console ｢data: 51d5a6e8-3c79-435e-a956-1657231daf4a｣ ｢n: 10000｣ Saved Visualization to: visualization.qzv ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | \_\_input\_ext | ` "input" ` | | \_\_q2galaxy\_\_GUI\_\_section\_\_extra\_opts\_\_ | ` {"n": "10000"} ` | | \_\_workflow\_invocation\_uuid\_\_ | ` "066906bc26e311ef89a8e76d21b9ab60" ` | | chromInfo | ` "/tmp/tmpo3e9ek65/galaxy-dev/tool-data/shared/ucsc/chrom/?.len" ` | | dbkey | ` "?" ` |

    • mvdbeek commented 3 months ago

    Is this stuck on anything ? Looks like the tests are all passing ?

    lldelisle commented 3 months ago
    bernt-matthias commented 3 months ago

    Only 3 of the 4 workflows have been updated (xref). Also wondering why the description field is changed.

    gxydevbot commented 3 weeks ago

    There are new updates, if you want to integrate them, close the PR and delete branch.

    gxydevbot commented 2 weeks ago

    There are new updates, if you want to integrate them, close the PR and delete branch.

    gxydevbot commented 1 week ago

    There are new updates, if you want to integrate them, close the PR and delete branch.

    gxydevbot commented 2 days ago

    There are new updates, if you want to integrate them, close the PR and delete branch.