Smartmatch is experimental at /pwd/NECAT/Linux-amd64/bin/Plgd/Project.pm line 232.

[Yunxia-li]

您好： 我运行了necat.pl config yyl@necat_cfg.txt 但是 error like : Smartmatch is experimental at /pwd/NECAT/Linux-amd64/bin/Plgd/Project.pm line 232. 然后也没有运行起来

_/pwd/NECAT/Linux-amd64/bin/Plgd/Project.pm line 232**.

226   sub waitScriptsGrid($$$$) {
227     my ($env, $cfg, $running, $part) = @_;
228
229     my @scripts = keys %$running;
230
231     my @finished = ();
232     until (@finished ~~ @scripts) {
233         @finished = ();
234         foreach my $s (@scripts) {
235             my $jobid = $running{$s};
236             my $state = checkScriptGrid($env, $cfg, $s, $jobid);
237             if ($state eq "" or $state eq "C") {
238                 if (waitScript($s, 5, 5, 1)) {
239                     push @finished, $s
240                 } else {
241                     plgdError("Failed to get script result, id=$jobid, $s")
242                 }
243             } else {
244                 sleep(5);
245             }
246         }
247         last if ($part and @finished > 0);
248     }
249     return @finished;
250 }

yyl@necat_cfg.txt

``PROJECT=yyl@necat ONT_READ_LIST=yyl.txt GENOME_SIZE=700k THREADS=20 MIN_READ_LENGTH=1000 OVLP_FAST_OPTIONS="-n 500 -z 20 -b 2000 -e 0.5 -j 0 -u 1 -a 1000" OVLP_SENSITIVE_OPTIONS="-n 500 -z 10 -e 0.5 -j 0 -u 1 -a 1000" CNS_FAST_OPTIONS="-a 2000 -x 4 -y 12 -l 1000 -e 0.5 -p 0.8 -u 0" CNS_SENSITIVE_OPTIONS="-a 2000 -x 4 -y 12 -l 1000 -e 0.5 -p 0.8 -u 0" TRIM_OVLP_OPTIONS="-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 1 -a 400" ASM_OVLP_OPTIONS="-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 0 -a 400" NUM_ITER=2 CNS_OUTPUT_COVERAGE=35 CLEANUP=0 USE_GRID=false GRID_NODE=0 FSA_OL_FILTER_OPTIONS="--max_overhang=-1 --min_identity=-1 --coverage=40" FSA_ASSEMBLE_OPTIONS="" FSA_CTG_BRIDGE_OPTIONS="--dump --read2ctg_min_identity=80 --read2ctg_min_coverage=4 --read2ctg_max_overhang=500 --read_min_length=5000 --ctg_min_length=1000 --read2ctg_min_aligned_length=5000 --select_branch=best" 有如下报错相关信息： http://www.freeoa.net/development/perl/perl-experimental-features-now-warn_2975.html https://metacpan.org/pod/release/RJBS/perl-5.18.0/pod/perldelta.pod#The_smartmatch_family_of_features_are_now_experimental

[wj1106]

我也遇到了这个问题，求解答

[xiaochuanle]

请加QQ群：316859622，开发者都在里面

在 2019-11-13 17:43:11，"wj1106" notifications@github.com 写道：

我也遇到了这个问题，求解答

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[wj1106]

好的，谢谢哈

在 2019-11-15 10:14:13，"Chuan-Le Xiao" notifications@github.com 写道： 请加QQ群：316859622，开发者都在里面

在 2019-11-13 17:43:11，"wj1106" notifications@github.com 写道：

我也遇到了这个问题，求解答

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[li0604]

这个问题您解决了吗？我也遇到类似问题：Smartmatch is experimental at /data/liqingmei/tools/NECAT/Linux-amd64/bin/Plgd/Project.pm line 263. 不知道怎么解决。

[zmz1988]

Dear Xiaochuan,

I recently ran NECAT, and also got a the same error as above. I thought the error has something to do with the Sun Grid Engine. But after I set USE_GRID=false, the error remains the same. I'm not sure how to solve this problem. Could you please help?

Thanks!

The error message:

Smartmatch is experimental at /home/NECAT/Linux-amd64/bin/Plgd/Project.pm line 263. 2021-03-10 15:04:47 [Info] Found Sun Grid Engine, which is /opt/gridengine File not Exist: ^_8B>^H^@^W<EFC`^@^C<92>$9v&

[xiaodan5]

这个问题您解决了吗？我也遇到类似问题：Smartmatch is experimental at /data/liqingmei/tools/NECAT/Linux-amd64/bin/Plgd/Project.pm line 263. 不知道怎么解决。

请问你的问题解决了吗？我也是line263有问题。

[wj1106]

没有，我换了别的组装方法。

在 2021-04-27 03:40:05，"xiaodan5" @.***> 写道：

这个问题您解决了吗？我也遇到类似问题：Smartmatch is experimental at /data/liqingmei/tools/NECAT/Linux-amd64/bin/Plgd/Project.pm line 263. 不知道怎么解决。

请问你的问题解决了吗？我也是line263有问题。

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[zmz1988]

I made a successful run now, and would like to write something here, in case somebody needs it.

After I got the error as mentioned below, I gave up installing NECAT by using git. In stead, I used miniconda3 to install necat, and it was successful. The Smartmatch line mentioned in the log is normal, which does not indicate errors. Error comes in the following lines, such as can't open file: contig.txt in /miniconda3/share/necat-0.0.1_update20200803-1/bin/Plgd/Project.pm. It took me a while to realise that the name of my config file (config but not contig) was wrong in the code. After I corrected the name, everything runs smoothly. This suggested that this error may come with the wrong input file or file name.

Dear Xiaochuan,

I recently ran NECAT, and also got a the same error as above. I thought the error has something to do with the Sun Grid Engine. But after I set USE_GRID=false, the error remains the same. I'm not sure how to solve this problem. Could you please help?

Thanks!

The error message:

Smartmatch is experimental at /home/NECAT/Linux-amd64/bin/Plgd/Project.pm line 263. 2021-03-10 15:04:47 [Info] Found Sun Grid Engine, which is /opt/gridengine File not Exist: ^_8B>^H^@^WC`^@^C<92$9v&

[xphab]

I have the same problem. I tried the binary and source code versions, as well as miniconda3, while line 263 errors are always there. Any suggestion is appreciated