-o outdir completely ignored, stdout appears to be in random order

[mw55309]

Hey

Sorry, me again.

1st, -o outdir is completely ignored. I just have an empty directory. Is that expected?

Also, here are two recent reports:

General summary:
Number of reads:        267802
Total bases:    881676364
Read length N50:        10026
Median read quality:    6.8
Active channels:        443
Mean read quality:      6.5
Mean read length:       3292.3
Median read length:     976.0
Number and percentage of reads above quality cutoffs
>Q5:    212748 (79.4%)
>Q7:    119014 (44.4%)
>Q10:   3672 (1.4%)
>Q12:   0 (0.0%)
>Q15:   0 (0.0%)
Top 5 longest reads and their mean basecall quality score
1:      58564 (8.9, [037d7ad7-007f-48f5-878c-c2cb8ab6f97f])
2:      51097 (8.6, [7c54cbc5-2024-467a-ace1-4b5fd6360ff7])
3:      49317 (7.3, [d3f0413a-b720-4e8d-8497-768a4e10a15c])
4:      49283 (6.6, [daa9ddeb-72f1-4200-b6d6-f465630199bc])
5:      47709 (6.0, [7af949f4-dc95-4782-9ff2-e0d8ac30c7f9])
Top 5 highest mean basecall quality scores and their read lengths
1:      11.7 (316, [566c3468-d65e-4aeb-a336-4ee0f50f59fa])
2:      11.7 (453, [650fa654-acc1-408e-93cc-5f7ebe0bc124])
3:      11.7 (275, [8609cce4-4b9b-4b34-9941-8433f2a83fb6])
4:      11.7 (517, [77ad56c3-3d78-4f27-8450-1f9fb681f738])
5:      11.6 (535, [0a98dc54-06be-4a05-b6d7-26980ea4ae87])

and

General summary:
Median read quality:    9.4
Total bases:    5019661393
Median read length:     3513.0
Active channels:        508
Number of reads:        888096
Mean read quality:      8.8
Mean read length:       5652.2
Read length N50:        10702
Top 5 highest mean basecall quality scores and their read lengths
1:      13.6 (1501, [23714233-9ff4-4606-ae70-a42ca1be5cf2])
2:      13.5 (424, [efc91728-5f0a-45ba-b5ed-40a4b0e0c7ea])
3:      13.4 (2835, [47811881-a073-4a4b-a2c9-29d23656b8c8])
4:      13.4 (670, [f4707154-4ba8-46fd-8806-42368a31e4b6])
5:      13.3 (827, [a2cbb2eb-57c4-4bbe-896f-ed2c95e20b41])
Number and percentage of reads above quality cutoffs
>Q5:    841485 (94.8%)
>Q7:    740976 (83.4%)
>Q10:   286963 (32.3%)
>Q12:   1352 (0.2%)
>Q15:   0 (0.0%)
Top 5 longest reads and their mean basecall quality score
1:      247156 (4.9, [bad76b0c-3987-4c00-9c52-0620144f0e63])
2:      247039 (5.0, [af44d792-b336-45b3-bf51-dd79deda1637])
3:      177927 (4.5, [a6cae286-4d36-428e-9f5a-99a93bfda1a6])
4:      140066 (4.4, [8509c8f4-55a9-4903-a596-597c0d4bdfe9])
5:      91587 (3.7, [24c291c7-d4c4-4575-953c-e36bed5bb83d])

So things appear to be coming out in random order - again, is that expected? Due to threading perhaps?

Cheers
Mick

[wdecoster]

Turns out I've added the -o option but haven't properly implemented it. Odd, will fix tonight or tomorrow.

The order of the output is because I use keys in a dictionary. I'll explicitly sort those, that absolutely makes more sense.

Thanks!

[wdecoster]

Hi Mick,

Both issues should be solved by updating NanoStat to 1.1.0.

Thanks again for reporting this. Please let me know if you encounter additional issues or have suggestions/feature requests.

Cheers,
Wouter

[mw55309]

Great, do you have a suggestion on how to upgrade my conda installation of 1.0 to the 1.1.0 available on github?

[wdecoster]

Pushing updates to PyPI/pip is easier/quicker for me than adapting the (bio)conda recipe, but you said installation using pip had failed? Would like to troubleshoot that, if possible.

PyPI should be "stable" versions. GitHub version should "almost always be quite okay but occasionally broken". Bioconda is updated "when there is a need for that but I tell myself I should do it more often".

But anyway, I should still go through the recipes and update the dependencies.