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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
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Final report not generated and need help understanding make preview #257

Closed ramay closed 4 years ago

ramay commented 4 years ago

Hi , I have run nullarbor on 24 Ecoli. The report failed to generate because it couldn't find the core.txt. Reading through other comments. I found out that I should run make preview to quickly look at the tree and quality of these samples. While the quality is good, the tree doesn't look that great.

The 10 samples labeled ECOLI 1-10 are obtained from the reference laboratory and we expect the other samples to be similar to them phylogenomically. My main interest is in virulence factors and AMR profiles of these samples but I thought it would be good to gather other information also. I can see that the information I need is in the resistome and virulome files but I would like to understand what is wrong that the report is not generating. Is there a way to not generate the core genome as these samples are different?

Thanks! Hena

Screen Shot 2020-02-12 at 10 18 56 AM
mabouelk commented 4 years ago

I hope you can find somebody to help you.

tseemann commented 4 years ago

@ramay thank you for using make preview first, that was a good idea. The preview report also should have another two tables with a distance matrix and a FASTQ/read summary. Look at the DEPTH column? What reference did you use?

ramay commented 4 years ago
I did look at the depth and they seem fine. Isolate Reads Yield GeeCee MinLen AvgLen MaxLen AvgQual Depth Quality
21B 3231886 477952597 50.5 60 147 151 32.7 101 ✔
21A 3921148 579998179 50.5 60 147 151 32.6 122 ✔
E_coli6 3348572 495105393 50.1 60 147 151 32.7 104 ✔
E_coli10 2701702 399396912 50.9 60 147 151 31.8 84 ✔
19A 2806318 414318036 50.7 60 147 151 32.6 87 ✔
143B 2599372 384314389 50.3 60 147 151 32.5 81 ✔
E_coli9 2923732 432150061 50.4 60 147 151 32.5 91 ✔
E_coli4 2555190 377968098 50 60 147 151 32.6 80 ✔
E_coli5 3460908 511519640 50 60 147 151 32.7 108 ✔
E_coli1 5619244 831699179 50.2 60 148 151 32.7 176 ✔
46B 2703996 399618787 50.3 60 147 151 32.6 84 ✔
77C 2535900 374782318 50 60 147 151 32.6 79 ✔
E_coli2 3658140 541010590 50.2 60 147 151 32.5 114 ✔
20B 4209336 622560384 49.8 60 147 151 32.7 131 ✔
111A 3184898 470707333 50.2 60 147 151 32.6 99 ✔
E_coli8 3200114 471797184 50 60 147 151 32.7 99 ✔
E_coli3 2890250 427277427 50.2 60 147 151 32.7 90 ✔
115C 3325746 490246319 50.3 60 147 151 32.6 103 ✔
E_coli7 3883120 574054141 50.4 60 147 151 32.7 121 ✔
55B 2554378 377792183 50.3 60 147 151 32.6 80 ✔
20A 2792552 412709687 49.8 60 147 151 32.7 87 ✔
111B 3674318 542280777 50.2 60 147 151 32.6 114 ✔
69C 2581400 381530619 50.3 60 147 151 32.5 80 ✔
55C 2621506 387354166 50.3 60 147 151 32.6 82 ✔
ramay commented 4 years ago

The reference used was used was ECOLI_GCF_000005845.2_ASM584v2_genomic.gbff. Thanks! Hena

tseemann commented 4 years ago

Your sequencing stats look ok. If you already ran a full nullarbor, you can look at denovo.tab to assess the assemblies too. Does that exist?

ramay commented 4 years ago

I managed to generate the report ! The problem was with snippy and samtool version conflict. I downloaded the latest version of snippy(4.5) after reading about it in snippy issues. Thanks for all your help! Hena

tseemann commented 4 years ago

@ramay glad to hear! thanks for letting me know.

dan-hud commented 4 years ago

I was also having this issue, server was running snippy 4.4.5, updating to the latest release (4.6) solved the issue.

tseemann commented 4 years ago

Thank you @dan-hud for letting us know, appreciated.