search

epi2me-labs / wf-single-cell

Other
69 stars 34 forks source link

ValueError: The expression matrix contains no cells #123

Closed sme229 closed 1 month ago

sme229 commented 1 month ago

Operating System

Other Linux (please specify below)

Other Linux

Linux 5.14.21-150400.24.28-default

Workflow Version

wf-single-cell v2.1.0-ga25ec6c

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

wf-single-cell v2.1.0-ga25ec6c

CLI command run

nextflow run epi2me-labs/wf-single-cell --expected_cells 3000 -profile singularity --fastq 'Elena-cDNA-2/20240624_1312_1D_PAW58377_76308a2c/fastq_pass' --kit_name '3prime' --kit_version 'v3' --ref_genome_dir 'OryCun_genome'

Workflow Execution - CLI Execution Profile

None

What happened?

Hello, I've got this error: Traceback (most recent call last): File "/home/sme229/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow-glue", line 7, in cli() File "/home/sme229/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow_glue/init.py", line 82, in cli args.func(args) File "/home/sme229/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow_glue/process_matrix.py", line 106, in main raise ValueError("""The expression matrix contains no cells. ValueError: The expression matrix contains no cells. This may indicate an issue with data quality or volume. Incorrectly specified 10x kits/versions and reference data can also lead to to removal of all data at this point. I couldn't find the exact same error in resolved issues. I also attach a screenshot my gtf file. gtf_file

Relevant log output

Jul-18 16:57:18.365 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:18.365 [Task submitter] INFO  nextflow.Session - [58/6dcefa] Submitted process > pipeline:process_bams:create_matrix (1606)
Jul-18 16:57:18.944 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6767; name: pipeline:process_bams:create_matrix (1599); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/c1/0e40d8ab84f9c0c95139d668c53dc5]
Jul-18 16:57:19.001 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:19.002 [Task submitter] INFO  nextflow.Session - [4c/7aacbf] Submitted process > pipeline:process_bams:create_matrix (1607)
Jul-18 16:57:19.565 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6768; name: pipeline:process_bams:create_matrix (1600); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/6c/1a7bf40b438063839d43a77d41a390]
Jul-18 16:57:19.574 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:19.574 [Task submitter] INFO  nextflow.Session - [60/72a54d] Submitted process > pipeline:process_bams:create_matrix (1608)
Jul-18 16:57:19.958 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6770; name: pipeline:process_bams:create_matrix (1602); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/1f/36ebaa1c53a4bfe83f781358533247]
Jul-18 16:57:19.978 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:19.978 [Task submitter] INFO  nextflow.Session - [27/4713a4] Submitted process > pipeline:process_bams:create_matrix (1609)
Jul-18 16:57:20.043 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6769; name: pipeline:process_bams:create_matrix (1601); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/5b/6cd34b48d5279b9f0e64bde238d93e]
Jul-18 16:57:20.083 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:20.083 [Task submitter] INFO  nextflow.Session - [54/d77238] Submitted process > pipeline:process_bams:create_matrix (1610)
Jul-18 16:57:21.835 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6771; name: pipeline:process_bams:create_matrix (1603); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/ea/74d91837bca74758a5a2191df924c1]
Jul-18 16:57:21.848 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:21.848 [Task submitter] INFO  nextflow.Session - [ea/d5feac] Submitted process > pipeline:process_bams:create_matrix (1611)
Jul-18 16:57:22.845 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6772; name: pipeline:process_bams:create_matrix (1604); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/74/42f2187798284ce946e0d5c53a7999]
Jul-18 16:57:22.851 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:22.851 [Task submitter] INFO  nextflow.Session - [ca/3c4794] Submitted process > pipeline:process_bams:create_matrix (1612)
Jul-18 16:57:22.961 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6773; name: pipeline:process_bams:create_matrix (1605); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/ea/8a97d8d1bcd22ce85832c1e6467cef]
Jul-18 16:57:22.967 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:22.967 [Task submitter] INFO  nextflow.Session - [74/996598] Submitted process > pipeline:process_bams:create_matrix (1613)
Jul-18 16:57:23.481 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6774; name: pipeline:process_bams:create_matrix (1606); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/58/6dcefa047ffb8b53055cacc7ed351d]
Jul-18 16:57:23.507 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:23.507 [Task submitter] INFO  nextflow.Session - [5a/a6ba70] Submitted process > pipeline:process_bams:create_matrix (1614)
Jul-18 16:57:24.374 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6775; name: pipeline:process_bams:create_matrix (1607); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/4c/7aacbf85f7da1f9a7325b6ac4e9363]
Jul-18 16:57:24.397 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:24.397 [Task submitter] INFO  nextflow.Session - [83/65bb15] Submitted process > pipeline:process_bams:create_matrix (1615)
Jul-18 16:57:24.621 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6776; name: pipeline:process_bams:create_matrix (1608); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/60/72a54dbf5823cea6c5c6b18320117a]
Jul-18 16:57:24.631 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:24.631 [Task submitter] INFO  nextflow.Session - [6c/228562] Submitted process > pipeline:process_bams:create_matrix (1616)
Jul-18 16:57:25.143 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6777; name: pipeline:process_bams:create_matrix (1609); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/27/4713a4db7f2c4ff593eb3c16a107c3]
Jul-18 16:57:25.152 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:25.152 [Task submitter] INFO  nextflow.Session - [f5/7b77d6] Submitted process > pipeline:process_bams:create_matrix (1617)
Jul-18 16:57:26.217 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6778; name: pipeline:process_bams:create_matrix (1610); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/54/d77238f485f95eee8b457098a93865]
Jul-18 16:57:26.225 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:26.225 [Task submitter] INFO  nextflow.Session - [43/0d36e1] Submitted process > pipeline:process_bams:create_matrix (1618)
Jul-18 16:57:26.845 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6779; name: pipeline:process_bams:create_matrix (1611); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/ea/d5feac88873df782092815d1dc0366]
Jul-18 16:57:26.852 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:26.852 [Task submitter] INFO  nextflow.Session - [5a/013ca6] Submitted process > pipeline:process_bams:create_matrix (1619)
Jul-18 16:57:27.745 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6781; name: pipeline:process_bams:create_matrix (1613); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/74/996598f3db3f6ac00a158ef788c49a]
Jul-18 16:57:27.757 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:27.758 [Task submitter] INFO  nextflow.Session - [20/23ad4e] Submitted process > pipeline:process_bams:create_matrix (1620)
Jul-18 16:57:28.088 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6780; name: pipeline:process_bams:create_matrix (1612); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/ca/3c479488ca6474278e854363c08e2b]
Jul-18 16:57:28.106 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:28.106 [Task submitter] INFO  nextflow.Session - [22/20d674] Submitted process > pipeline:process_bams:create_matrix (1621)
Jul-18 16:57:28.351 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6782; name: pipeline:process_bams:create_matrix (1614); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/5a/a6ba708cf87b2efc411896301dcbe5]
Jul-18 16:57:28.392 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:28.392 [Task submitter] INFO  nextflow.Session - [63/4293fe] Submitted process > pipeline:process_bams:create_matrix (1622)
Jul-18 16:57:29.216 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6783; name: pipeline:process_bams:create_matrix (1615); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/83/65bb1587c59d0a99045392292ec35e]
Jul-18 16:57:29.224 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:29.224 [Task submitter] INFO  nextflow.Session - [03/145f79] Submitted process > pipeline:process_bams:create_matrix (1623)
Jul-18 16:57:29.573 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6784; name: pipeline:process_bams:create_matrix (1616); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/6c/228562fd5c5a4ceed82055638a55c6]
Jul-18 16:57:29.580 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:29.580 [Task submitter] INFO  nextflow.Session - [97/49a4da] Submitted process > pipeline:process_bams:create_matrix (1624)
Jul-18 16:57:30.032 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6785; name: pipeline:process_bams:create_matrix (1617); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/f5/7b77d692260ddedaa0cf3474fbb6b2]
Jul-18 16:57:30.040 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:30.040 [Task submitter] INFO  nextflow.Session - [59/665819] Submitted process > pipeline:process_bams:create_matrix (1625)
Jul-18 16:57:31.209 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6786; name: pipeline:process_bams:create_matrix (1618); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/43/0d36e1c5e596ec4898e527cf09aa12]
Jul-18 16:57:31.231 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:31.231 [Task submitter] INFO  nextflow.Session - [aa/9d551f] Submitted process > pipeline:process_bams:create_matrix (1626)
Jul-18 16:57:32.034 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6787; name: pipeline:process_bams:create_matrix (1619); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/5a/013ca6e0a72bc591ff651c04360534]
Jul-18 16:57:32.047 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:32.047 [Task submitter] INFO  nextflow.Session - [df/4edc14] Submitted process > pipeline:process_bams:create_matrix (1627)
Jul-18 16:57:32.618 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6788; name: pipeline:process_bams:create_matrix (1620); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/20/23ad4ec05397cff120dd636e15facc]
Jul-18 16:57:32.625 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:32.625 [Task submitter] INFO  nextflow.Session - [23/cdf3b0] Submitted process > pipeline:process_bams:create_matrix (1628)
Jul-18 16:57:33.156 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6789; name: pipeline:process_bams:create_matrix (1621); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/22/20d674df069b17e11662793966fa85]
Jul-18 16:57:33.164 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:33.164 [Task submitter] INFO  nextflow.Session - [6f/68b552] Submitted process > pipeline:process_bams:create_matrix (1629)
Jul-18 16:57:33.203 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6790; name: pipeline:process_bams:create_matrix (1622); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/63/4293fe6f6d79344d65287ee4290355]
Jul-18 16:57:33.214 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:33.214 [Task submitter] INFO  nextflow.Session - [58/8e5d71] Submitted process > pipeline:process_bams:create_matrix (1630)
Jul-18 16:57:34.453 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6791; name: pipeline:process_bams:create_matrix (1623); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/03/145f7906830b494443cbd2506b6ebb]
Jul-18 16:57:34.473 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:34.473 [Task submitter] INFO  nextflow.Session - [06/0285e5] Submitted process > pipeline:process_bams:create_matrix (1631)
Jul-18 16:57:34.487 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6792; name: pipeline:process_bams:create_matrix (1624); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/97/49a4dab05efbaa7d06cac5b2ed1dcd]
Jul-18 16:57:34.494 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:34.494 [Task submitter] INFO  nextflow.Session - [7b/3cdcdf] Submitted process > pipeline:process_bams:create_matrix (1632)
Jul-18 16:57:34.934 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6793; name: pipeline:process_bams:create_matrix (1625); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/59/665819f8ad405b28be2b6ead9c60f4]
Jul-18 16:57:34.944 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:34.944 [Task submitter] INFO  nextflow.Session - [d4/28e37f] Submitted process > pipeline:process_bams:create_matrix (1633)
Jul-18 16:57:36.303 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6794; name: pipeline:process_bams:create_matrix (1626); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/aa/9d551f3f3c64bfa4badaa4c0446b87]
Jul-18 16:57:36.312 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:36.312 [Task submitter] INFO  nextflow.Session - [94/5e30d5] Submitted process > pipeline:process_bams:create_matrix (1634)
Jul-18 16:57:36.934 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6795; name: pipeline:process_bams:create_matrix (1627); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/df/4edc14acad6076381998a860375e47]
Jul-18 16:57:36.941 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:36.941 [Task submitter] INFO  nextflow.Session - [b6/39890d] Submitted process > pipeline:process_bams:create_matrix (1635)
Jul-18 16:57:37.485 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6796; name: pipeline:process_bams:create_matrix (1628); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/23/cdf3b03505f551f4f2d53ad5b9f489]
Jul-18 16:57:37.536 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:37.537 [Task submitter] INFO  nextflow.Session - [f7/f28079] Submitted process > pipeline:process_bams:create_matrix (1636)
Jul-18 16:57:38.062 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6798; name: pipeline:process_bams:create_matrix (1630); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/58/8e5d7108956aeff64873ae64f6f398]
Jul-18 16:57:38.065 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6797; name: pipeline:process_bams:create_matrix (1629); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/6f/68b5523aa51688bcf1f928e8548948]
Jul-18 16:57:38.078 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:38.078 [Task submitter] INFO  nextflow.Session - [17/eb4fa9] Submitted process > pipeline:process_bams:create_matrix (1637)
Jul-18 16:57:38.085 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:38.085 [Task submitter] INFO  nextflow.Session - [8e/a127a4] Submitted process > pipeline:process_bams:create_matrix (1638)
Jul-18 16:57:39.444 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6800; name: pipeline:process_bams:create_matrix (1632); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/7b/3cdcdf8e28bd47c0b20622f155c69e]
Jul-18 16:57:39.453 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:39.453 [Task submitter] INFO  nextflow.Session - [40/8a025b] Submitted process > pipeline:process_bams:create_matrix (1639)
Jul-18 16:57:39.471 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6799; name: pipeline:process_bams:create_matrix (1631); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/06/0285e5d05651365d01980872aabecc]
Jul-18 16:57:39.479 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:39.479 [Task submitter] INFO  nextflow.Session - [d1/d3d30b] Submitted process > pipeline:process_bams:create_matrix (1640)
Jul-18 16:57:39.910 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6801; name: pipeline:process_bams:create_matrix (1633); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/d4/28e37fe0d531139843b46ad2f5c994]
Jul-18 16:57:39.920 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:39.921 [Task submitter] INFO  nextflow.Session - [26/8c0b68] Submitted process > pipeline:process_bams:create_matrix (1641)
Jul-18 16:57:41.865 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6802; name: pipeline:process_bams:create_matrix (1634); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/94/5e30d51c304aa330d88b0463d92a36]
Jul-18 16:57:41.942 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6803; name: pipeline:process_bams:create_matrix (1635); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/b6/39890d90252b28f7c3031b31a22481]
Jul-18 16:57:41.943 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:41.943 [Task submitter] INFO  nextflow.Session - [e5/9e7036] Submitted process > pipeline:process_bams:create_matrix (1642)
Jul-18 16:57:41.951 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:41.951 [Task submitter] INFO  nextflow.Session - [5e/3f298d] Submitted process > pipeline:process_bams:create_matrix (1643)
Jul-18 16:57:42.530 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6804; name: pipeline:process_bams:create_matrix (1636); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/f7/f28079de11f4a34e411ebb348fb7a5]
Jul-18 16:57:42.537 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:42.537 [Task submitter] INFO  nextflow.Session - [52/2c4def] Submitted process > pipeline:process_bams:create_matrix (1645)
Jul-18 16:57:43.144 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6805; name: pipeline:process_bams:create_matrix (1637); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/17/eb4fa94df9b3598423d625042c4ae1]
Jul-18 16:57:43.150 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6806; name: pipeline:process_bams:create_matrix (1638); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/8e/a127a4c1bc4ef8ee182dea10d0becd]
Jul-18 16:57:43.153 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:43.153 [Task submitter] INFO  nextflow.Session - [e0/e4c49c] Submitted process > pipeline:process_bams:create_matrix (1644)
Jul-18 16:57:43.162 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:43.162 [Task submitter] INFO  nextflow.Session - [34/b966b7] Submitted process > pipeline:process_bams:create_matrix (1646)
Jul-18 16:57:44.392 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6807; name: pipeline:process_bams:create_matrix (1639); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/40/8a025b662c72666a762887dc819b2e]
Jul-18 16:57:44.428 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:44.428 [Task submitter] INFO  nextflow.Session - [ce/5e70c7] Submitted process > pipeline:process_bams:create_matrix (1647)
Jul-18 16:57:44.625 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6808; name: pipeline:process_bams:create_matrix (1640); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/d1/d3d30b5868a93efdab5215d6b983f7]
Jul-18 16:57:44.635 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:44.635 [Task submitter] INFO  nextflow.Session - [84/fb8bbe] Submitted process > pipeline:process_bams:create_matrix (1648)
Jul-18 16:57:44.704 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6809; name: pipeline:process_bams:create_matrix (1641); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/26/8c0b68278f7694c90c8fa89737a022]
Jul-18 16:57:44.715 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:44.715 [Task submitter] INFO  nextflow.Session - [fd/dbc14d] Submitted process > pipeline:process_bams:create_matrix (1650)
Jul-18 16:57:46.830 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6810; name: pipeline:process_bams:create_matrix (1642); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/e5/9e7036ed08dd9ac8b0b91d65532fa8]
Jul-18 16:57:46.836 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:46.836 [Task submitter] INFO  nextflow.Session - [d2/c50e3c] Submitted process > pipeline:process_bams:create_matrix (1651)
Jul-18 16:57:46.837 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6811; name: pipeline:process_bams:create_matrix (1643); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/5e/3f298d5555ecf42de8281e69df3255]
Jul-18 16:57:46.843 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:46.844 [Task submitter] INFO  nextflow.Session - [a4/9290fd] Submitted process > pipeline:process_bams:create_matrix (1652)
Jul-18 16:57:47.396 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6813; name: pipeline:process_bams:create_matrix (1645); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/52/2c4def449c48d38dfa53c48fee40fe]
Jul-18 16:57:47.411 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:47.411 [Task submitter] INFO  nextflow.Session - [2b/9247b6] Submitted process > pipeline:process_bams:create_matrix (1653)
Jul-18 16:57:48.078 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6812; name: pipeline:process_bams:create_matrix (1644); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/e0/e4c49c80f6e9efcd5b5b95b2281667]
Jul-18 16:57:48.086 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:48.086 [Task submitter] INFO  nextflow.Session - [2e/6623c0] Submitted process > pipeline:process_bams:create_matrix (1654)
Jul-18 16:57:48.171 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6814; name: pipeline:process_bams:create_matrix (1646); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/34/b966b73c02bc56c650b795b9d63683]
Jul-18 16:57:48.179 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:48.179 [Task submitter] INFO  nextflow.Session - [e5/fb5989] Submitted process > pipeline:process_bams:create_matrix (1655)
Jul-18 16:57:49.405 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6815; name: pipeline:process_bams:create_matrix (1647); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/ce/5e70c7b00f45603218af7a03e5d2ac]
Jul-18 16:57:49.422 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:49.422 [Task submitter] INFO  nextflow.Session - [60/2ae8d5] Submitted process > pipeline:process_bams:create_matrix (1656)
Jul-18 16:57:49.585 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6818; name: pipeline:process_bams:create_matrix (1650); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/fd/dbc14dc1deef2d904e9a877d1ce405]
Jul-18 16:57:49.592 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:49.592 [Task submitter] INFO  nextflow.Session - [05/e27502] Submitted process > pipeline:process_bams:create_matrix (1657)
Jul-18 16:57:49.617 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6816; name: pipeline:process_bams:create_matrix (1648); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/84/fb8bbe2ad956f3ddece08925b964cd]
Jul-18 16:57:49.632 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:49.632 [Task submitter] INFO  nextflow.Session - [68/93e3b5] Submitted process > pipeline:process_bams:create_matrix (1658)
Jul-18 16:57:51.967 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6819; name: pipeline:process_bams:create_matrix (1651); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/d2/c50e3c77056efe82d6defabc6d0eec]
Jul-18 16:57:51.976 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:51.976 [Task submitter] INFO  nextflow.Session - [40/d8c5b8] Submitted process > pipeline:process_bams:create_matrix (1659)
Jul-18 16:57:52.394 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6821; name: pipeline:process_bams:create_matrix (1653); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/2b/9247b65f225be8eaaaf59cffe5bae9]
Jul-18 16:57:52.405 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:52.405 [Task submitter] INFO  nextflow.Session - [78/ddd27f] Submitted process > pipeline:process_bams:create_matrix (1660)
Jul-18 16:57:52.526 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6820; name: pipeline:process_bams:create_matrix (1652); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/a4/9290fdeb03dd63d1c1a0aaf738f3c5]
Jul-18 16:57:52.534 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:52.534 [Task submitter] INFO  nextflow.Session - [48/78995c] Submitted process > pipeline:process_bams:create_matrix (1661)
Jul-18 16:57:52.891 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6822; name: pipeline:process_bams:create_matrix (1654); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/2e/6623c0b9296e1c8bf8d762a303d43c]
Jul-18 16:57:52.930 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:52.930 [Task submitter] INFO  nextflow.Session - [d0/8b357e] Submitted process > pipeline:process_bams:create_matrix (1662)
Jul-18 16:57:53.482 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6823; name: pipeline:process_bams:create_matrix (1655); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/e5/fb59899a2f3bf54c2d79340f9914c9]
Jul-18 16:57:54.425 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6825; name: pipeline:process_bams:create_matrix (1657); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/05/e2750241e3c3927bac35717af0aa58]
Jul-18 16:57:54.509 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:54.509 [Task submitter] INFO  nextflow.Session - [98/686f34] Submitted process > pipeline:process_bams:merge_transcriptome (1)
Jul-18 16:57:54.791 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6826; name: pipeline:process_bams:create_matrix (1658); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/68/93e3b54ddc632bbdccf17fa0c1301e]
Jul-18 16:57:55.610 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6824; name: pipeline:process_bams:create_matrix (1656); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/60/2ae8d57686470e9a3aca39852e76b6]
Jul-18 16:57:56.988 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6828; name: pipeline:process_bams:create_matrix (1660); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/78/ddd27f5d55eb1a4179e35018d6996d]
Jul-18 16:57:57.078 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6829; name: pipeline:process_bams:create_matrix (1661); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/48/78995c34b86aca389d27f9b4ba5687]
Jul-18 16:57:57.226 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6827; name: pipeline:process_bams:create_matrix (1659); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/40/d8c5b80f0dc6af81c6343a0d8b4b0c]
Jul-18 16:57:57.531 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6830; name: pipeline:process_bams:create_matrix (1662); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/d0/8b357e518cbf7c9dac9c11a964136e]
Jul-18 16:57:58.705 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:58.705 [Task submitter] INFO  nextflow.Session - [80/9e4d85] Submitted process > pipeline:process_bams:combine_final_tag_files (1)
Jul-18 16:57:58.747 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:58.747 [Task submitter] INFO  nextflow.Session - [1b/be7e05] Submitted process > pipeline:process_bams:tag_bam (1)
Jul-18 16:57:58.798 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:57:58.798 [Task submitter] INFO  nextflow.Session - [73/9b28a8] Submitted process > pipeline:process_bams:process_matrix (2)
Jul-18 16:57:58.799 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below
~> TaskHandler[id: 6833; name: pipeline:process_bams:process_matrix (1); status: NEW; exit: -; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/64/8e10a1c073340173be900c0b33b9d6]
Jul-18 16:58:28.897 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6831; name: pipeline:process_bams:merge_transcriptome (1); status: COMPLETED; exit: 0; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/98/686f3480370b8d063dc3ab49b91dbf]
Jul-18 16:58:28.943 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jul-18 16:58:28.943 [Task submitter] INFO  nextflow.Session - [64/8e10a1] Submitted process > pipeline:process_bams:process_matrix (1)
Jul-18 16:58:50.099 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6835; name: pipeline:process_bams:process_matrix (2); status: COMPLETED; exit: 1; error: -; workDir: /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/73/9b28a800caee7992aa7a3d7fff02a6]
Jul-18 16:58:50.103 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=pipeline:process_bams:process_matrix (2); work-dir=/datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/73/9b28a800caee7992aa7a3d7fff02a6
  error [nextflow.exception.ProcessFailedException]: Process `pipeline:process_bams:process_matrix (2)` terminated with an error exit status (1)
Jul-18 16:58:50.120 [TaskFinalizer-3] ERROR nextflow.processor.TaskProcessor - Error executing process > 'pipeline:process_bams:process_matrix (2)'

Caused by:
  Process `pipeline:process_bams:process_matrix (2)` terminated with an error exit status (1)

Command executed:

  export NUMBA_NUM_THREADS=1
  workflow-glue process_matrix         inputs/matrix*.hdf         --feature gene         --raw gene_raw_feature_bc_matrix         --processed gene_processed_feature_bc_matrix         --per_cell_mito gene.expression.mito-per-cell.tsv         --per_cell_expr gene.expression.mean-per-cell.tsv         --umap_tsv gene.expression.umap.tsv         --enable_filtering         --min_features 200         --min_cells 3         --max_mito 20         --mito_prefixes MT-         --norm_count 10000         --enable_umap         --replicates 3

Command exit status:
  1

Command output:
  (empty)

Command error:
  [16:58:08 - workflow_glue] Bootstrapping CLI.
  /home/epi2melabs/conda/lib/python3.8/site-packages/umap/distances.py:1063: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
    @numba.jit()
  /home/epi2melabs/conda/lib/python3.8/site-packages/umap/distances.py:1071: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
    @numba.jit()
  /home/epi2melabs/conda/lib/python3.8/site-packages/umap/distances.py:1086: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
    @numba.jit()
  /home/epi2melabs/conda/lib/python3.8/site-packages/umap/umap_.py:660: NumbaDeprecationWarning: The 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.
    @numba.jit()
  [16:58:21 - workflow_glue] Starting entrypoint.
  [16:58:21 - workflow_glue.AggreMatri] Constructing count matrices
  [16:58:49 - workflow_glue.AggreMatri] Removing unknown features.
  Traceback (most recent call last):
    File "/home/sme229/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow-glue", line 7, in <module>
      cli()
    File "/home/sme229/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow_glue/__init__.py", line 82, in cli
      args.func(args)
    File "/home/sme229/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow_glue/process_matrix.py", line 106, in main
      raise ValueError("""The expression matrix contains no cells.
  ValueError: The expression matrix contains no cells.
              This may indicate an issue with data quality or volume.
              Incorrectly specified 10x kits/versions and reference data can also lead to
              to removal of all data at this point.

Work dir:
  /datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/work/73/9b28a800caee7992aa7a3d7fff02a6

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Jul-18 16:58:50.124 [TaskFinalizer-3] DEBUG nextflow.Session - Session aborted -- Cause: Process `pipeline:process_bams:process_matrix (2)` terminated with an error exit status (1)
Jul-18 16:58:50.135 [TaskFinalizer-3] DEBUG nextflow.Session - The following nodes are still active:
[process] pipeline:process_bams:umi_gene_saturation
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:process_bams:pack_images
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:prepare_report_data
  status=ACTIVE
  port 0: (queue) OPEN  ; channel: -
  port 1: (cntrl) -     ; channel: $

[process] pipeline:makeReport
  status=ACTIVE
  port 0: (value) bound ; channel: metadata
  port 1: (value) bound ; channel: versions
  port 2: (value) bound ; channel: params.csv
  port 3: (value) bound ; channel: stats
  port 4: (queue) OPEN  ; channel: survival.tsv
  port 5: (value) OPEN  ; channel: umap_dirs
  port 6: (value) OPEN  ; channel: images
  port 7: (value) bound ; channel: umap_genes
  port 8: (value) bound ; channel: wf_version
  port 9: (cntrl) -     ; channel: $

Jul-18 16:58:50.184 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jul-18 16:58:51.352 [main] DEBUG nextflow.Session - Session await > all processes finished
Jul-18 16:58:51.352 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jul-18 16:58:51.369 [Actor Thread 30] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jul-18 16:58:51.371 [Actor Thread 27] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=pipeline:prepare_report_data; work-dir=null
  error [java.lang.InterruptedException]: java.lang.InterruptedException
Jul-18 16:58:51.680 [main] WARN  n.processor.TaskPollingMonitor - Killing running tasks (3)
Jul-18 16:58:51.697 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=6831; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=3; succeedDuration=2d 18h 6m 57s; failedDuration=51.3s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=8; peakCpus=16; peakMemory=46.5 GB; ]
Jul-18 16:58:51.697 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jul-18 16:58:51.698 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jul-18 16:58:52.982 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jul-18 16:58:53.438 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jul-18 16:58:53.486 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

nrhorner commented 1 month ago

Hi @sme229

The error message below tells us that the expression matrix is empty

The expression matrix contains no cells.
This may indicate an issue with data quality or volume.
Incorrectly specified 10x kits/versions and reference data can also lead to
to removal of all data at this point.

Have you specified the correct kit and version? Does the reference sequence have the correct matching annotation? How many reads are trying to process?

sme229 commented 1 month ago

Hello @nrhorner Thanks for looking into this. The kit version is actually v3.1, I'll try to run with 3.1 instead of 3. This is how my reference fasta file looks like: image

sme229 commented 1 month ago

I modified the headers in my reference file and that seemed to solve the issue, but I get a different error now. I'll open a new issue