mapping values are not allowed here

[anubhabkhan]

Hey,

My parameter file is:

Output directory: GADMA/Output_sort_all_seq Input data: input.vcf, pop_order_new.txt Outgroup: False Sequence length:{HiC_scaffold_1: 100107381, HiC_scaffold_2: 105422710, HiC_scaffold_3: 84653302, HiC_scaffold_4: 71730761, HiC_scaffold_5: 82087087, HiC_scaffold_6: 72648741, HiC_scaffold_7: 206147042, HiC_scaffold_8: 75724504, HiC_scaffold_9: 42998131, HiC_scaffold_10: 56992115, HiC_scaffold_11: 68020579, HiC_scaffold_12: 69753810, HiC_scaffold_13: 174872996, HiC_scaffold_14: 125785404, HiC_scaffold_15: 95956831, HiC_scaffold_16: 92867347, HiC_scaffold_17: 25658408, HiC_scaffold_18: 72251902, HiC_scaffold_19: 70704222, HiC_scaffold_20: 58087477, HiC_scaffold_21: 66824428, HiC_scaffold_22: 65113277, HiC_scaffold_23: 99334673, HiC_scaffold_24: 206517395, HiC_scaffold_25: 119051098, HiC_scaffold_26: 169401614, HiC_scaffold_27: 144118974}

but I get the error:

File "/usr/local/bin/gadma", line 11, in sys.exit(main()) File "/usr/local/lib/python3.6/site-packages/gadma/core/core.py", line 51, in main settings_storage, args = arg_parser.get_settings() File "/usr/local/lib/python3.6/site-packages/gadma/cli/arg_parser.py", line 127, in get_settings settings_storage = SettingsStorage.from_file(args.params, args.extra) File "/usr/local/lib/python3.6/site-packages/gadma/cli/settings_storage.py", line 1017, in from_file return obj.update_from_file(param_file, extra_param_file) File "/usr/local/lib/python3.6/site-packages/gadma/cli/settings_storage.py", line 972, in update_from_file ruamel.yaml.RoundTripLoader) File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/main.py", line 951, in load return loader._constructor.get_single_data() File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/constructor.py", line 111, in get_single_data node = self.composer.get_single_node() File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/composer.py", line 78, in get_single_node document = self.compose_document() File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/composer.py", line 101, in compose_document node = self.compose_node(None, None) File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/composer.py", line 138, in compose_node node = self.compose_mapping_node(anchor) File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/composer.py", line 218, in compose_mapping_node item_value = self.compose_node(node, item_key) File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/composer.py", line 111, in compose_node if self.parser.check_event(AliasEvent): File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/parser.py", line 140, in check_event self.current_event = self.state() File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/parser.py", line 603, in parse_block_mapping_value if self.scanner.check_token(ValueToken): File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/scanner.py", line 1764, in check_token self._gather_comments() File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/scanner.py", line 1806, in _gather_comments self.fetch_more_tokens() File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/scanner.py", line 283, in fetch_more_tokens return self.fetch_value() File "/usr/local/lib/python3.6/site-packages/ruamel/yaml/scanner.py", line 656, in fetch_value self.reader.get_mark(), ruamel.yaml.scanner.ScannerError: mapping values are not allowed here in "GADMA_param_sort_all1.par", line 4, column 59

Could you please help?

Thanks Anubhab

[noscode]

Hi,

Try to add space after Sequence length:_{HiC_scaffold..., without space file reader is confused. (_ means just " ")

Best regards, Ekaterina

[anubhabkhan]

Aha! Thank you so much for the prompt responses

On 22 Sep 2022, at 17:51, Ekaterina Noskova @.***> wrote:

Hi,

Try to add space after Sequence length:, without space file reader is confused.

Best regards, Ekaterina

— Reply to this email directly, view it on GitHub https://github.com/ctlab/GADMA/issues/76#issuecomment-1254945929, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFU7WMP7SDG2JUJHN7OML7DV7RFMNANCNFSM6AAAAAAQS7Q4K4. You are receiving this because you authored the thread.

[anubhabkhan]

Hey Ekaterina,

Sorry to bother you with this particular question. I used a filtered mutli chromosome vcf file as an input for the GADMA run. What should be the value of L for my run? Should it be the number of SNP loci? or should it be the length of the whole autosomal genome size?

thanks again anubhab

On 22 Sep 2022, at 17:52, ANUBHAB KHAN @.***> wrote:

Aha! Thank you so much for the prompt responses

On 22 Sep 2022, at 17:51, Ekaterina Noskova @.*** @.***>> wrote:

Hi,

Try to add space after Sequence length:, without space file reader is confused.

Best regards, Ekaterina

— Reply to this email directly, view it on GitHub https://github.com/ctlab/GADMA/issues/76#issuecomment-1254945929, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFU7WMP7SDG2JUJHN7OML7DV7RFMNANCNFSM6AAAAAAQS7Q4K4. You are receiving this because you authored the thread.

[noscode]

Hi Anubhab,

L is the same as sequence length. So as you specified it already you are good. If you have met L in code then L is the total length of used sequence.

Best regards, Ekaterina