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iqbal-lab-org / pandora

Pan-genome inference and genotyping with long noisy or short accurate reads
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tsv file for pandora compare #213

Closed LilithElina closed 2 years ago

LilithElina commented 4 years ago

This is not a big issue, but maybe you could mention somewhere that the tsv file you give to pandora compare needs an empty line at the end? I was very confused because I only got 26 out of my 27 samples compared, until I added a new line at the end of my list.

mbhall88 commented 4 years ago

Hmm, that sounds odd. Would you be able to share your TSV file so we can fix this?

iqbal-lab commented 4 years ago

Thats a classic bug, cortex always used to do that, it split the input file by \n, and if the final line of the file did not have /n, it didn't get read.

iqbal-lab commented 4 years ago

sorry, that was a comment not anything helpful;

LilithElina commented 4 years ago

That's probably it, but if you still want the file(s), here you go:

ESP067  ../../sample_data/ESP067_S142_L002_R1_001.fastq.gz
MHH1679 ../../sample_data/MHH16798_S65_L001_R1_001.fastq.gz
CH4528  ../../sample_data/CH4528_S2_L001_R1_001.fastq.gz
ZG8038  ../../sample_data/ZG8038581181_S40_L001_R1_001.fastq.gz
CH4591  ../../sample_data/CH4591_S12_L001_R1_001.fastq.gz
CH2706  ../../sample_data/CH2706_S19_L001_R1_001.fastq.gz
MHH1605 ../../sample_data/MHH16050_S18_L001_R1_001.fastq.gz
MHH1770 ../../sample_data/MHH17704_S142_R1_001.fastq.gz
F1959   ../../sample_data/F1959_S44_L001_R1_001.fastq.gz
CH2682  ../../sample_data/CH2682_S11_L001_R1_001.fastq.gz
ZG8510  ../../sample_data/ZG8510487_S96_L001_R1_001.fastq.gz
ESP027  ../../sample_data/ESP027_S125_L002_R1_001.fastq.gz
F2166   ../../sample_data/F2166_S79_L001_R1_001.fastq.gz
F2006   ../../sample_data/F2006_S13_L001_R1_001.fastq.gz
CH2860  ../../sample_data/CH2860_R1.fastq.gz
MHH1776 ../../sample_data/MHH17767_S42_L001_R1_001.fastq.gz
F2059   ../../sample_data/F2059_S30_L001_R1_001.fastq.gz
ESP088  ../../sample_data/ESP088_S86_L001_R1_001.fastq.gz
F2224   ../../sample_data/F2224_S130_R1_001.fastq.gz
F2856   ../../sample_data/F2856_S136_R1_001.fastq.gz
ZG3167  ../../sample_data/ZG316717_S50_L001_R1_001.fastq.gz
F1864   ../../sample_data/F1864_S4_L001_R1_001.fastq.gz
MHH1656 ../../sample_data/MHH16563_S14_L001_R1_001.fastq.gz
CH4634  ../../sample_data/CH4634_S11_L001_R1_001.fastq.gz
ESP046  ../../sample_data/ESP046_S129_L002_R1_001.fastq.gz
ZG3023  ../../sample_data/ZG302383_S68_L001_R1_001.fastq.gz
F2020   ../../sample_data/F2020_S37_L001_R1_001.fastq.gz

At first, the F2020 line was the last one, so F2020 was not included in my comparison. This changed with the addition of a new line after that one.

leoisl commented 2 years ago

Closed via https://github.com/rmcolq/pandora/pull/285