ERROR:root:--extsize must >= 1! and chipseq.bds can not get all replicates go through about chipseq_pipeline HOT 25 CLOSED

Hi Jin, Thanks for your reply. But unfortunately, I got lost. Would you please send me the link on how to run it? For example, I used to run it as "bds /home/ysun/TF_chipseq_pipeline/chipseq.bds”. Thank you so much for your help. Best, Ying On Oct 25, 2019, at 12:09 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: It looks like the estimated fragment length is negative. This pipeline is no longer maintained. Please use https://github.com/ENCODE-DCC/chip-seq-pipeline2. I think this issue is already fixed in the new pipeline. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7ED6FLFGMGPKPD5UZ3QQM75BA5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECJJCPA#issuecomment-546476348>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7FK2UD3SPL7UREF6MLQQM75BANCNFSM4JE7KTUQ>.

Dear Jin, I followed the link you suggested and installed everything. What I am trying to do is to run chip-seq-pipeline2 on our local Linux server. Unfortunately, I got the following error message which I cannot figure out how to fix it. I don’t quite get what [wdl] should I use here. Confused. Would you please help me to solve it? Just for your convenience, I also attached my json file below. Thank you very much for your time and help. I really appreciate it a lot! Best, Ying =============================================================== [ysun@gatsby sub1]$ caper run chip-seq-pipeline2 -i testHg19.json [CaperURI] read from local, src: /nfs/lab/ysun/GSE128072_ChIP/sub1/testHg19.json [CaperURI] read from local, src: /nfs/lab/ysun/chip-seq-pipeline2-genome/hg19/hg19.tsv Traceback (most recent call last): File "/home/ysun/.local/bin/caper", line 13, in <module> main() File "/home/ysun/.local/lib/python3.6/site-packages/caper/caper.py", line 1266, in main c.run() File "/home/ysun/.local/lib/python3.6/site-packages/caper/caper.py", line 201, in run imports_file = self.__create_imports_zip_file_from_wdl(tmp_dir) File "/home/ysun/.local/lib/python3.6/site-packages/caper/caper.py", line 842, in __create_imports_zip_file_from_wdl imports = self.__find_val_from_wdl(Caper.RE_PATTERN_WDL_IMPORT) File "/home/ysun/.local/lib/python3.6/site-packages/caper/caper.py", line 1043, in __find_val_from_wdl with open(CaperURI(self._wdl).get_local_file(), 'r') as fp: FileNotFoundError: [Errno 2] No such file or directory: '/nfs/lab/ysun/GSE128072_ChIP/sub1/chip-seq-pipeline2' =============================================================== testHg19.json { "chip.title" : "H3K27acB1 (single-end)", "chip.description" : "This is a test run of B1 H3K27ac for GSE128072 for single-end sample.", "chip.pipeline_type" : "histone", "chip.aligner" : "bowtie2", "chip.align_only" : false, "chip.true_rep_only" : false, "chip.genome_tsv" : "/nfs/lab/ysun/chip-seq-pipeline2-genome/hg19/hg19.tsv", "chip.paired_end" : true, "chip.ctl_paired_end" : true, "chip.always_use_pooled_ctl" : false, "chip.fastqs_rep1" : [ "SRR8701823.fastq.gz", "SRR8701824.fastq.gz", "SRR8701825.fastq.gz", "SRR8701826.fastq.gz", "SRR8701827.fastq.gz", "SRR8701828.fastq.gz", "SRR8701829.fastq.gz" , "SRR8701830.fastq.gz", "SRR8701831.fastq.gz", "SRR8701832.fastq.gz", "SRR8701833.fastq.gz", "SRR8701834.fastq.gz" ], "chip.ctl_fastqs_rep1" : [ "SRR8702202.fastq.gz", "SRR8702203.fastq.gz", "SRR8702204.fastq.gz", "SRR8702205.fastq.gz", "SRR8702206.fastq.gz", "SRR8702207.fastq.gz", "SRR8702208.fastq .gz" ] } On Oct 25, 2019, at 3:28 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: Please read through README on https://github.com/ENCODE-DCC/chip-seq-pipeline2. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7ADCMZ7TDSRV3MLE5DQQNXH3A5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECJW7DY#issuecomment-546533263>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7GXQARW3RKNKFCAFA3QQNXH3ANCNFSM4JE7KTUQ>.

Thanks for your prompt respond. I changed the command as "caper run chip.wdl -i testHg19.json”. And I also changed an error in my .json file (single-end instead of paired-end). But I still got the following error message. Any suggestions will be appreciated. Thanks again. Best, Ying ================================================================================ (encode-chip-seq-pipeline) [ysun@gatsby sub1]$ caper run chip.wdl -i testHg19.json [CaperURI] read from local, src: /nfs/lab/ysun/GSE128072_ChIP/sub1/testHg19.json Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/bin/caper", line 13, in <module> main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/caper/caper.py", line 1266, in main c.run() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/caper/caper.py", line 197, in run input_file = self.__create_input_json_file(tmp_dir) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/caper/caper.py", line 680, in __create_input_json_file uri_type=uri_type, uri_exts=self._deepcopy_ext) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/caper/caper_uri.py", line 811, in deepcopy uri_type=uri_type, uri_exts=uri_exts) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/caper/caper_uri.py", line 776, in __deepcopy_json org_d = json.loads(contents, object_pairs_hook=OrderedDict) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/json/__init__.py", line 361, in loads return cls(**kw).decode(s) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 13 column 29 (char 423) On Dec 5, 2019, at 12:37 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: It should be caper run chip-seq-pipeline2/chip.wdl -i testHg19.json — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7HYESLMISBLFYGKVUTQXFQ7XA5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGCCAGI#issuecomment-562307097>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7B4ZOYNBVTQLGICA53QXFQ7XANCNFSM4JE7KTUQ>.

Thanks. I caught the typo and right now it’s running as following. Does it look normal to you? Thanks. Best, Ying ================================ [ysun@gatsby sub1]$ conda activate encode-chip-seq-pipeline (encode-chip-seq-pipeline) [ysun@gatsby sub1]$ caper run chip.wdl -i testHg19.json [CaperURI] read from local, src: /nfs/lab/ysun/GSE128072_ChIP/sub1/testHg19.json [CaperURI] read from local, src: /nfs/lab/ysun/chip-seq-pipeline2-genome/hg19/hg19.tsv [CaperURI] copying from url to local, src: https://github.com/broadinstitute/cromwell/releases/download/47/cromwell-47.jar [CaperURI] wait 30 sec for file being unlocked. retries: 1, max_retries: 100. uri: /home/ysun/.caper/cromwell_jar/cromwell-47.jar [CaperURI] wait 30 sec for file being unlocked. retries: 2, max_retries: 100. uri: /home/ysun/.caper/cromwell_jar/cromwell-47.jar [CaperURI] wait 30 sec for file being unlocked. retries: 3, max_retries: 100. uri: /home/ysun/.caper/cromwell_jar/cromwell-47.jar [CaperURI] wait 30 sec for file being unlocked. retries: 4, max_retries: 100. uri: /home/ysun/.caper/cromwell_jar/cromwell-47.jar [CaperURI] wait 30 sec for file being unlocked. retries: 5, max_retries: 100. uri: /home/ysun/.caper/cromwell_jar/cromwell-47.jar On Dec 5, 2019, at 2:39 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: Check line 13 column 29 of your input JSON. Check commas, brackets, ... For example, TAB is not allowed in JSON. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7B7TDU7IBWBKV6XOKTQXF7KVA5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGCMU3A#issuecomment-562350700>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7F2CVT2WAQOQGSDT5TQXF7KVANCNFSM4JE7KTUQ>.

It’s running. Thanks! On Dec 5, 2019, at 3:44 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: Delete lock file /home/ysun/.caper/cromwell_jar/*.lock and try again. Make sure that you have only one process to run a pipeline. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7EYOXU6ZCMVJDE3FFLQXGG7DA5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGCRARA#issuecomment-562368580>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7C3MOXLSR6NLO5VICTQXGG7DANCNFSM4JE7KTUQ>.

Hi Jin, I am trying to use Croo to organize chip-seq-pipeline2 output as following but got error message too. Please advise what I should do to fix ti. Thank you so much and have a nice weekend! Best, Ying =================== (encode-chip-seq-pipeline) [ysun@gatsby GSE128072_ChIP]$ croo /nfs/lab/ysun/GSE128072_ChIP/chip/d531476f-00a3-488f-8589-5d2653b385d4/call-qc_report/execution/qc.json[this is the only json file I can find in the output folder. Is this the right on e to use?] --out-def-json summaryTestHg19.json --out-dir testBucket Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/bin/croo", line 13, in <module> main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/croo.py", line 299, in main soft_link=args['method'] == 'link') File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/croo.py", line 52, in __init__ self._cm = CromwellMetadata(self._metadata) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/cromwell_metadata.py", line 94, in __init__ self._workflow_id = self._metadata_json['id'] KeyError: 'id' On Dec 5, 2019, at 3:44 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: Delete lock file /home/ysun/.caper/cromwell_jar/*.lock and try again. Make sure that you have only one process to run a pipeline. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7EYOXU6ZCMVJDE3FFLQXGG7DA5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGCRARA#issuecomment-562368580>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7C3MOXLSR6NLO5VICTQXGG7DANCNFSM4JE7KTUQ>.

Thanks Jin! I found the metadata.json, however, I still got error message: ============== (encode-chip-seq-pipeline) [ysun@gatsby GSE128072_ChIP]$ croo chip/e496c521-6b96-47a1-b47c-cb8ab1416730/metadata.json --out-def-json test.json --out-dir testBucket Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/bin/croo", line 13, in <module> main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/croo.py", line 299, in main soft_link=args['method'] == 'link') File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/croo.py", line 52, in __init__ self._cm = CromwellMetadata(self._metadata) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/cromwell_metadata.py", line 100, in __init__ self.__parse_calls(self._metadata_json['calls']) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/cromwell_metadata.py", line 179, in __parse_calls all_outputs=tuple(out_files), TypeError: 'NoneType' object is not iterable ============== Please advise. Thank you so much. Best, Ying On Dec 6, 2019, at 7:14 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: Find metadata.json instead of qc.json. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7E6KMSV47LVIO4RTQTQXMIIVA5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGF4M7Y#issuecomment-562808447>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7EBZU4BEKZXHM3S7TTQXMIIVANCNFSM4JE7KTUQ>.

Another question is: The output has been stored in a default folder like “./chip/e496c521-6b96-47a1-b47c-cb8ab1416730(or similar long string)/“. I am wondering if I can give a more meaningful name instead of using the long name? Best, Ying On Dec 6, 2019, at 7:14 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: Find metadata.json instead of qc.json. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7E6KMSV47LVIO4RTQTQXMIIVA5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGF4M7Y#issuecomment-562808447>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7EBZU4BEKZXHM3S7TTQXMIIVANCNFSM4JE7KTUQ>.

I tried to go through the output folder but can not find "*.pval.signal.bigwig" in "/chip/e496c521-6b96-47a1-b47c-cb8ab1416730//call-macs2_signal_track/shard-0/execution/" but only “*.merged.nodup_x_ctl_for_rep1.fc.signal.bigwig”. Would you please let me know what I did wrong here? Thanks a lot! Best, Ying On Dec 6, 2019, at 7:14 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: Find metadata.json instead of qc.json. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7E6KMSV47LVIO4RTQTQXMIIVA5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGF4M7Y#issuecomment-562808447>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7EBZU4BEKZXHM3S7TTQXMIIVANCNFSM4JE7KTUQ>.

Use croo to organize caper s raw outputs

My Croo does not work properly for some reasons. On Dec 9, 2019, at 11:32 AM, Ying Sun <[email protected]<mailto:[email protected]>> wrote: Thanks Jin! I found the metadata.json, however, I still got error message: ============== (encode-chip-seq-pipeline) [ysun@gatsby GSE128072_ChIP]$ croo chip/e496c521-6b96-47a1-b47c-cb8ab1416730/metadata.json --out-def-json test.json --out-dir testBucket Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/bin/croo", line 13, in <module> main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/croo.py", line 299, in main soft_link=args['method'] == 'link') File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/croo.py", line 52, in __init__ self._cm = CromwellMetadata(self._metadata) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/cromwell_metadata.py", line 100, in __init__ self.__parse_calls(self._metadata_json['calls']) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/cromwell_metadata.py", line 179, in __parse_calls all_outputs=tuple(out_files), TypeError: 'NoneType' object is not iterable ============== Please advise. Thank you so much. Best, Ying On Dec 6, 2019, at 7:14 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: Find metadata.json instead of qc.json. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7E6KMSV47LVIO4RTQTQXMIIVA5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGF4M7Y#issuecomment-562808447>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7EBZU4BEKZXHM3S7TTQXMIIVANCNFSM4JE7KTUQ>.

Sorry, but still no luck. ===================================== (encode-chip-seq-pipeline) [ysun@gatsby GSE128072_ChIP]$ croo -v 0.3.3 (encode-chip-seq-pipeline) [ysun@gatsby GSE128072_ChIP]$ croo chip/e496c521-6b96-47a1-b47c-cb8ab1416730/metadata.json --out-def-json test.json --out-dir testBucket Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/bin/croo", line 13, in <module> main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/croo.py", line 304, in main no_graph=args['no_graph']) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/croo.py", line 53, in __init__ self._cm = CromwellMetadata(self._metadata) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/cromwell_metadata.py", line 100, in __init__ self.__parse_calls(self._metadata_json['calls']) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline/lib/python3.7/site-packages/croo/cromwell_metadata.py", line 183, in __parse_calls for output_name, output_path, _ in out_files: TypeError: 'NoneType' object is not iterable ===================================== Best, Ying On Dec 9, 2019, at 1:09 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: Can you upgrade croo to 0.3.3 and try again? pip install croo==0.3.3 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7GPVYHFBVGLYCK4XYDQX2XZ7A5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGKWVMQ#issuecomment-563440306>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7HEIVSNG4S75YVQF43QX2XZ7ANCNFSM4JE7KTUQ>.

After the replacement, it works perfectly fine. Thank you so much for your help. Best, Ying On Dec 9, 2019, at 2:28 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: Can you find/modify your cromwell_metadata.py like the following? How to find it: leepc12@kadru:/users/leepc12/code/croo$ python Python 3.7.3 (default, Mar 27 2019, 22:11:17) [GCC 7.3.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information.

'/users/leepc12/code/croo/croo/cromwell_metadata.py'

Replace this (from line 183) for output_name, output_path, _ in out_files: # add each output file to DAG n = CMNode( type='output', shard_idx=shard_idx, task_name=task_name, output_name=output_name, output_path=output_path, all_outputs=None, all_inputs=None) self._dag.add_node(n) with this if out_files: for output_name, output_path, _ in out_files: # add each output file to DAG n = CMNode( type='output', shard_idx=shard_idx, task_name=task_name, output_name=output_name, output_path=output_path, all_outputs=None, all_inputs=None) self._dag.add_node(n) If this works, I will make a hot fix. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7BBZ2NZXESMHAHOV3TQX3BAPA5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGK5Y6Q#issuecomment-563469434>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7D2MUGS2SJDVYH3EI3QX3BAPANCNFSM4JE7KTUQ>.

Hi Jin, I have one more question. I am wondering if you can help me to figure it out. If I activated conda directly on the server and ran the pipeline, it worked totally fine. The commands I used as below just FYI: ----- conda activate encode-chip-seq-pipeline caper run chip.wdl -i B10H3K27acHg19.json ----- Since I have many similar jobs, and I want to run them in the background use bash script. However, the bash script did not work (ran using nohup). ----- #!/bin/sh conda activate encode-chip-seq-pipeline caper run chip.wdl -i B10H3K27acHg19.json ----- It seems that I did not activate the conda correctly. I am not very familiar with conda and wondering if you have any idea what should I do to achieve it? I am sorry to bother you that often and much and really appreciate all your help. Best regards, Ying On Dec 10, 2019, at 11:33 AM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: That sounds good. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7CUUVBQ7P27S2QAUW3QX7VIHA5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGQSECQ#issuecomment-564208138>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7FYKPQFIWXJL5VSYFDQX7VIHANCNFSM4JE7KTUQ>.

Got it! Thanks! Best, Ying On Dec 10, 2019, at 4:01 PM, Jin Lee <[email protected]<mailto:[email protected]>> wrote: It's Conda's issue. Conda has changed its activation method from source activate to conda activate. source activate worked fine in a BASH script but conda activate doesn't. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#48?email_source=notifications&email_token=AHEKV7BWADASUCEAX7MPYRDQYAUXPA5CNFSM4JE7KTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGRMJMY#issuecomment-564315315>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHEKV7BAJ4S4DZQFR4UBDMLQYAUXPANCNFSM4JE7KTUQ>.