search

qiita-spots / qiita

Qiita - A multi-omics databasing effort
http://qiita.microbio.me
BSD 3-Clause "New" or "Revised" License
120 stars 80 forks source link

run_prefix values do not match your sample names #2126

Closed colinbrislawn closed 7 years ago

colinbrislawn commented 7 years ago

On qiita study 11114 while running 'Split libraries FASTQ', I just got this error. 

ValueError: Some run_prefix values do not match your sample names:

This makes sense because my fastq file names have dashes in them T2--16-20 and my sample_names have periods T2..16.20 I made them different on purpose and was not expecting this error.

Does the run_prefix of each sample have to match the sample_name? There is no mention of this in the documentation on run_prefix. If they have to match, why include run_prefix at all?

Thanks for helping me out.

antgonza commented 7 years ago

I think you are hitting this: https://github.com/qiita-spots/qp-target-gene/issues/10, cause the run prefix should be exact, so for example one of them should be: T3-3_R1.

colinbrislawn commented 7 years ago

OK. If this is the intended functionality, I'll rename and upload my files.

I can submit a PR adding this as an explicit requirement to the docs.

Thanks!

colinbrislawn commented 7 years ago

Can you check on study 11114 again? I'm getting this error:

Some run_prefix values do not match your sample names: T31R, T21115R, ... But qiita shows these sample names including 11114.T21115R and 11114.T31R.

Is run_prefix supposed to include the sample ID? I can upload my files for a third time, and I would also like feedback on the right way to do this to I can contribute better to the docs.

Thanks for helping me fix this.

ackermag commented 7 years ago

Hi Colin I have attached a template for per sample fastq that worked for me. Note that there are forward and reverse files for each sample and they linked correctly.

Are you sure you have a sample for each of the run files? (Just asking because I made this mistake once.) Gail

On Fri, May 5, 2017 at 1:44 PM, Colin Brislawn notifications@github.com wrote:

Can you check on study 11114 https://qiita.ucsd.edu/study/description/11114 again? I'm getting this error:

Some run_prefix values do not match your sample names: T31R, T21115R, ... But qiita shows these sample names including 11114.T21115R and 11114.T31R.

Is run_prefix supposed to include the sample ID? I can upload my files for a third time, and I would also like feedback on the right way to do this to I can contribute better to the docs.

Thanks for helping me fix this.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/biocore/qiita/issues/2126#issuecomment-299571126, or mute the thread https://github.com/notifications/unsubscribe-auth/AB69gA1VZN9mJTOjvg_nuH2Kdu5OebQFks5r24o4gaJpZM4NO1uC .

-- Gail Ackermann Knight Lab UCSD glackermann@ucsd.edu ackermag@ucsd.edu

sample_name instrument_model qiita_prep_id run_prefix run_file 10817.10689.2.blank.wateri Illumina HiSeq 4000 2556 P2_blank_wateri_S58_L002 P2_blank_wateri_S58_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.blank.waterii Illumina HiSeq 4000 2556 P2_blank_waterii_S59_L002 P2_blank_wateri_S58_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.blank.wateriii Illumina HiSeq 4000 2556 P2_blank_wateriii_S60_L002 P2_blank_waterii_S59_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.blank.wateriv Illumina HiSeq 4000 2556 P2_blank_wateriv_S61_L002 P2_blank_waterii_S59_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.blank.waterv Illumina HiSeq 4000 2556 P2_blank_waterv_S62_L002 P2_blank_wateriii_S60_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.blank.watervi Illumina HiSeq 4000 2556 P2_blank_watervi_S63_L002 P2_blank_wateriii_S60_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.blank.watervii Illumina HiSeq 4000 2556 P2_blank_watervii_S64_L002 P2_blank_wateriv_S61_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.blanki Illumina HiSeq 4000 2556 P2_blanki_S68_L002 P2_blank_wateriv_S61_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.blankii Illumina HiSeq 4000 2556 P2_blankii_S69_L002 P2_blank_waterv_S62_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.blankiii Illumina HiSeq 4000 2556 P2_blankiii_S76_L002 P2_blank_waterv_S62_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.blankiv Illumina HiSeq 4000 2556 P2_blankiv_S77_L002 P2_blank_watervi_S63_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.1.Bs5000i Illumina HiSeq 4000 2556 P2_Bs5000i_S78_L002 P2_blank_watervi_S63_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.1.Bs5000ii Illumina HiSeq 4000 2556 P2_Bs5000ii_S79_L002 P2_blank_watervii_S64_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.1.Bs5000iii Illumina HiSeq 4000 2556 P2_Bs5000iii_S80_L002 P2_blank_watervii_S64_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.1.Bs500i Illumina HiSeq 4000 2556 P2_Bs500i_S70_L002 P2_blanki_S68_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.1.Bs500ii Illumina HiSeq 4000 2556 P2_Bs500ii_S71_L002 P2_blanki_S68_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.1.Bs500iii Illumina HiSeq 4000 2556 P2_Bs500iii_S72_L002 P2_blankii_S69_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.1.Bs50i Illumina HiSeq 4000 2556 P2_Bs50i_S73_L002 P2_blankii_S69_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.1.Bs50ii Illumina HiSeq 4000 2556 P2_Bs50ii_S74_L002 P2_blankiii_S76_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.1.Bs50iii Illumina HiSeq 4000 2556 P2_Bs50iii_S75_L002 P2_blankiii_S76_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.1.Bs5i Illumina HiSeq 4000 2556 P2_Bs5i_S65_L002 P2_blankiv_S77_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.1.Bs5ii Illumina HiSeq 4000 2556 P2_Bs5ii_S66_L002 P2_blankiv_S77_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.1.Bs5iii Illumina HiSeq 4000 2556 P2_Bs5iii_S67_L002 P2_Bs5000i_S78_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.FC1 Illumina HiSeq 4000 2556 P2_FC1_S26_L002 P2_Bs5000i_S78_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.FC2 Illumina HiSeq 4000 2556 P2_FC2_S22_L002 P2_Bs5000ii_S79_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.FC3 Illumina HiSeq 4000 2556 P2_FC3_S42_L002 P2_Bs5000ii_S79_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.FC5 Illumina HiSeq 4000 2556 P2_FC5_S7_L002 P2_Bs5000iii_S80_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.001 Illumina HiSeq 4000 2556 P2_JPL_SAF_001_S9_L002 P2_Bs5000iii_S80_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.002 Illumina HiSeq 4000 2556 P2_JPL_SAF_002_S57_L002 P2_Bs500i_S70_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.005 Illumina HiSeq 4000 2556 P2_JPL_SAF_005_S1_L002 P2_Bs500i_S70_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.007 Illumina HiSeq 4000 2556 P2_JPL_SAF_007_S34_L002 P2_Bs500ii_S71_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.008 Illumina HiSeq 4000 2556 P2_JPL_SAF_008_S27_L002 P2_Bs500ii_S71_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.010 Illumina HiSeq 4000 2556 P2_JPL_SAF_010_S17_L002 P2_Bs500iii_S72_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.014 Illumina HiSeq 4000 2556 P2_JPL_SAF_014_S15_L002 P2_Bs500iii_S72_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.017 Illumina HiSeq 4000 2556 P2_JPL_SAF_017_S6_L002 P2_Bs50i_S73_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.018 Illumina HiSeq 4000 2556 P2_JPL_SAF_018_S47_L002 P2_Bs50i_S73_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.020 Illumina HiSeq 4000 2556 P2_JPL_SAF_020_S23_L002 P2_Bs50ii_S74_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.022 Illumina HiSeq 4000 2556 P2_JPL_SAF_022_S20_L002 P2_Bs50ii_S74_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.023 Illumina HiSeq 4000 2556 P2_JPL_SAF_023_S14_L002 P2_Bs50iii_S75_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.026 Illumina HiSeq 4000 2556 P2_JPL_SAF_026_S38_L002 P2_Bs50iii_S75_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.029 Illumina HiSeq 4000 2556 P2_JPL_SAF_029_S30_L002 P2_Bs5i_S65_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.032 Illumina HiSeq 4000 2556 P2_JPL_SAF_032_S35_L002 P2_Bs5i_S65_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.036 Illumina HiSeq 4000 2556 P2_JPL_SAF_036_S21_L002 P2_Bs5ii_S66_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.038 Illumina HiSeq 4000 2556 P2_JPL_SAF_038_S12_L002 P2_Bs5ii_S66_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.039 Illumina HiSeq 4000 2556 P2_JPL_SAF_039_S32_L002 P2_Bs5iii_S67_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.040 Illumina HiSeq 4000 2556 P2_JPL_SAF_040_S31_L002 P2_Bs5iii_S67_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.041 Illumina HiSeq 4000 2556 P2_JPL_SAF_041_S8_L002 P2_FC1_S26_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.046 Illumina HiSeq 4000 2556 P2_JPL_SAF_046_S49_L002 P2_FC1_S26_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.047 Illumina HiSeq 4000 2556 P2_JPL_SAF_047_S24_L002 P2_FC2_S22_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.051 Illumina HiSeq 4000 2556 P2_JPL_SAF_051_S10_L002 P2_FC2_S22_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.053 Illumina HiSeq 4000 2556 P2_JPL_SAF_053_S50_L002 P2_FC3_S42_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.054 Illumina HiSeq 4000 2556 P2_JPL_SAF_054_S29_L002 P2_FC3_S42_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.055 Illumina HiSeq 4000 2556 P2_JPL_SAF_055_S45_L002 P2_FC5_S7_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.059 Illumina HiSeq 4000 2556 P2_JPL_SAF_059_S52_L002 P2_FC5_S7_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.060 Illumina HiSeq 4000 2556 P2_JPL_SAF_060_S16_L002 P2_JPL_SAF_001_S9_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.062 Illumina HiSeq 4000 2556 P2_JPL_SAF_062_S33_L002 P2_JPL_SAF_001_S9_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.063 Illumina HiSeq 4000 2556 P2_JPL_SAF_063_S48_L002 P2_JPL_SAF_002_S57_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.065 Illumina HiSeq 4000 2556 P2_JPL_SAF_065_S54_L002 P2_JPL_SAF_002_S57_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.066 Illumina HiSeq 4000 2556 P2_JPL_SAF_066_S56_L002 P2_JPL_SAF_005_S1_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.067 Illumina HiSeq 4000 2556 P2_JPL_SAF_067_S44_L002 P2_JPL_SAF_005_S1_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.068 Illumina HiSeq 4000 2556 P2_JPL_SAF_068_S5_L002 P2_JPL_SAF_007_S34_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.073 Illumina HiSeq 4000 2556 P2_JPL_SAF_073_S25_L002 P2_JPL_SAF_007_S34_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.075 Illumina HiSeq 4000 2556 P2_JPL_SAF_075_S37_L002 P2_JPL_SAF_008_S27_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.077 Illumina HiSeq 4000 2556 P2_JPL_SAF_077_S11_L002 P2_JPL_SAF_008_S27_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.079 Illumina HiSeq 4000 2556 P2_JPL_SAF_079_S18_L002 P2_JPL_SAF_010_S17_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.080 Illumina HiSeq 4000 2556 P2_JPL_SAF_080_S55_L002 P2_JPL_SAF_010_S17_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.081 Illumina HiSeq 4000 2556 P2_JPL_SAF_081_S2_L002 P2_JPL_SAF_014_S15_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.083 Illumina HiSeq 4000 2556 P2_JPL_SAF_083_S3_L002 P2_JPL_SAF_014_S15_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.085 Illumina HiSeq 4000 2556 P2_JPL_SAF_085_S53_L002 P2_JPL_SAF_017_S6_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.089 Illumina HiSeq 4000 2556 P2_JPL_SAF_089_S19_L002 P2_JPL_SAF_017_S6_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.090 Illumina HiSeq 4000 2556 P2_JPL_SAF_090_S36_L002 P2_JPL_SAF_018_S47_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.091 Illumina HiSeq 4000 2556 P2_JPL_SAF_091_S13_L002 P2_JPL_SAF_018_S47_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.094 Illumina HiSeq 4000 2556 P2_JPL_SAF_094_S4_L002 P2_JPL_SAF_020_S23_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.096 Illumina HiSeq 4000 2556 P2_JPL_SAF_096_S46_L002 P2_JPL_SAF_020_S23_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.098 Illumina HiSeq 4000 2556 P2_JPL_SAF_098_S43_L002 P2_JPL_SAF_022_S20_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.JPL.SAF.099 Illumina HiSeq 4000 2556 P2_JPL_SAF_099_S39_L002 P2_JPL_SAF_022_S20_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.JPL.SAF.100 Illumina HiSeq 4000 2556 P2_JPL_SAF_100_S51_L002 P2_JPL_SAF_023_S14_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.NC2 Illumina HiSeq 4000 2556 P2_NC2_S41_L002 P2_JPL_SAF_023_S14_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.NC3 Illumina HiSeq 4000 2556 P2_NC3_S40_L002 P2_JPL_SAF_026_S38_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.NC4 Illumina HiSeq 4000 2556 P2_NC4_S28_L002 P2_JPL_SAF_026_S38_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.Vf.0.05 Illumina HiSeq 4000 2556 P2_Vf_0_05_S88_L002 P2_JPL_SAF_029_S30_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.Vf.0.5 Illumina HiSeq 4000 2556 P2_Vf_0_5_S87_L002 P2_JPL_SAF_029_S30_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.Vf.125 Illumina HiSeq 4000 2556 P2_Vf_125_S91_L002 P2_JPL_SAF_032_S35_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.Vf.16 Illumina HiSeq 4000 2556 P2_Vf_16_S94_L002 P2_JPL_SAF_032_S35_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.Vf.250 Illumina HiSeq 4000 2556 P2_Vf_250_S90_L002 P2_JPL_SAF_036_S21_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.Vf.31 Illumina HiSeq 4000 2556 P2_Vf_31_S93_L002 P2_JPL_SAF_036_S21_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.Vf.4 Illumina HiSeq 4000 2556 P2_Vf_4_S96_L002 P2_JPL_SAF_038_S12_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.Vf.5 Illumina HiSeq 4000 2556 P2_Vf_5_S86_L002 P2_JPL_SAF_038_S12_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.Vf.50 Illumina HiSeq 4000 2556 P2_Vf_50_S85_L002 P2_JPL_SAF_039_S32_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.Vf.500 Illumina HiSeq 4000 2556 P2_Vf_500_S84_L002 P2_JPL_SAF_039_S32_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.Vf.5000 Illumina HiSeq 4000 2556 P2_Vf_5000_S83_L002 P2_JPL_SAF_040_S31_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.Vf.50000 Illumina HiSeq 4000 2556 P2_Vf_50000_S82_L002 P2_JPL_SAF_040_S31_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.Vf.500000 Illumina HiSeq 4000 2556 P2_Vf_500000_S81_L002 P2_JPL_SAF_041_S8_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.Vf.500ii Illumina HiSeq 4000 2556 P2_Vf_500ii_S89_L002 P2_JPL_SAF_041_S8_L002_R2_001.fastq.gz (raw reverse seqs) 10817.10689.2.Vf.63 Illumina HiSeq 4000 2556 P2_Vf_63_S92_L002 P2_JPL_SAF_046_S49_L002_R1_001.fastq.gz (raw forward seqs) 10817.10689.2.Vf.8 Illumina HiSeq 4000 2556 P2_Vf_8_S95_L002 P2_JPL_SAF_046_S49_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_047_S24_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_047_S24_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_051_S10_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_051_S10_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_053_S50_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_053_S50_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_054_S29_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_054_S29_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_055_S45_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_055_S45_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_059_S52_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_059_S52_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_060_S16_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_060_S16_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_062_S33_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_062_S33_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_063_S48_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_063_S48_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_065_S54_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_065_S54_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_066_S56_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_066_S56_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_067_S44_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_067_S44_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_068_S5_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_068_S5_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_073_S25_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_073_S25_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_075_S37_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_075_S37_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_077_S11_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_077_S11_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_079_S18_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_079_S18_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_080_S55_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_080_S55_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_081_S2_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_081_S2_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_083_S3_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_083_S3_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_085_S53_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_085_S53_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_089_S19_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_089_S19_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_090_S36_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_090_S36_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_091_S13_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_091_S13_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_094_S4_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_094_S4_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_096_S46_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_096_S46_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_098_S43_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_098_S43_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_099_S39_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_099_S39_L002_R2_001.fastq.gz (raw reverse seqs) P2_JPL_SAF_100_S51_L002_R1_001.fastq.gz (raw forward seqs) P2_JPL_SAF_100_S51_L002_R2_001.fastq.gz (raw reverse seqs) P2_NC2_S41_L002_R1_001.fastq.gz (raw forward seqs) P2_NC2_S41_L002_R2_001.fastq.gz (raw reverse seqs) P2_NC3_S40_L002_R1_001.fastq.gz (raw forward seqs) P2_NC3_S40_L002_R2_001.fastq.gz (raw reverse seqs) P2_NC4_S28_L002_R1_001.fastq.gz (raw forward seqs) P2_NC4_S28_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_0_05_S88_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_0_05_S88_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_0_5_S87_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_0_5_S87_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_125_S91_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_125_S91_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_16_S94_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_16_S94_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_250_S90_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_250_S90_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_31_S93_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_31_S93_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_4_S96_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_4_S96_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_5_S86_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_5_S86_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_50_S85_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_50_S85_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_500_S84_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_500_S84_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_5000_S83_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_5000_S83_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_50000_S82_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_50000_S82_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_500000_S81_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_500000_S81_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_500ii_S89_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_500ii_S89_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_63_S92_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_63_S92_L002_R2_001.fastq.gz (raw reverse seqs) P2_Vf_8_S95_L002_R1_001.fastq.gz (raw forward seqs) P2_Vf_8_S95_L002_R2_001.fastq.gz (raw reverse seqs)

colinbrislawn commented 7 years ago

Hello Gail,

I'm trying to follow the instructions for Per sample FASTQ files, but I'm having a lot of trouble.

EDIT: Thanks for attaching that file, Gail. Let me see if I can get that format working.

colinbrislawn commented 7 years ago

I have another question about this error: ValueError: Some run_prefix values do not match your sample names:

Does sample_names refer to 1) the names of the files you uploaded, 2) to the sample_name column of the sample info file, or 3) the sample_name column of the prep info file?

colinbrislawn commented 7 years ago

Thanks for the example template Gail. Here is the version I tried:

sample_name primer  barcode run_prefix  center_name platform    instrument_model    library_construction_protocol   experiment_design_description
11114.T31R  AA  AA  T31R    Pacific Northwest National Labs Illumina    Illumina MiSeq  16S v4 EMP primers, 150 bp paired-end reads with overlap    Multi kingdom microbiome succession and founder species
...

I think all my sample names match, but I got the same error.

screen shot 2017-05-16 at 12 46 57 pm
ackermag commented 7 years ago

Hi Colin I will take a look and get back to you. To answer your question the sample names in the error is the sample_name in both the prep and sample file (that have to match) and the run_prefix is the file name (without .fastq) which also has to match in some way. I think you may be confusing instructions for with barcode info vs without.

On Tue, May 16, 2017 at 11:53 AM, Colin Brislawn notifications@github.com wrote:

I have another question about this error: ValueError: Some run_prefix values do not match your sample names:

Does sample_names refer to 1) the names of the files you uploaded, 2) to the sample_name column of the sample info file, or 3) the sample_name column of the prep info file?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/biocore/qiita/issues/2126#issuecomment-301879808, or mute the thread https://github.com/notifications/unsubscribe-auth/AB69gGbXCYkHEpjNd7Q165H1m0ZS0YJSks5r6fCwgaJpZM4NO1uC .

-- Gail Ackermann Knight Lab UCSD glackermann@ucsd.edu ackermag@ucsd.edu

colinbrislawn commented 7 years ago

Oh, maybe my sample_names in the sample info file no long match after playing with my prep info.

Let me look around some more...

EDIT: I just updated both my sample info and prep info files, and am still receiving this error. Thank you for your help. I totally need it 😞

ackermag commented 7 years ago

You may need to change the run files so 'R' is not in the runprefix (because R1 and R2 are forward and reverse. Did you select the option for fastq with barcodes? Then you will have to concatenate the run files, strip the barcodes and upload a barcodes file.

On Tue, May 16, 2017 at 3:28 PM, Colin Brislawn notifications@github.com wrote:

Oh, maybe my sample_names in the sample info file no long match after playing with my prep info.

Let me look around some more...

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/biocore/qiita/issues/2126#issuecomment-301933673, or mute the thread https://github.com/notifications/unsubscribe-auth/AB69gLoDiK3TgGTe5C0_4Br7jidUuJitks5r6iL5gaJpZM4NO1uC .

-- Gail Ackermann Knight Lab UCSD glackermann@ucsd.edu ackermag@ucsd.edu

colinbrislawn commented 7 years ago

Gail, I don't have primers or barcodes in my fastq files. For each one of my samples, I have a pair of fastq files, and I think this should match the format for per_sample_fastq.

The documentation says

have the uploaded sequence file(s) name in the run_prefix field. This should be an exact match without extension (fastq or fastq.gz).

Your example prep info file does not include the _R1_ suffix, so I'm confused. Your example does include run_file, but I don't see that documented anywhere.

Earlier, @antgonza mentioned that this might be a bug. Should I try passing full file names (with R1 suffix) to avoid this bug?

ackermag commented 7 years ago

Yes - try that.

On Tue, May 16, 2017 at 6:08 PM, Colin Brislawn notifications@github.com wrote:

Gail, I don't have primers or barcodes in my fastq files. For each one of my samples, I have a pair of fastq files, and I think this should match the format for per_sample_fastq https://qiita.ucsd.edu/static/doc/html/tutorials/no-raw-sequences.html#per-sample-fastq-files-without-barcode-and-primer-information .

The documentation says

have the uploaded sequence file(s) name in the run_prefix field. This should be an exact match without extension (fastq or fastq.gz).

Your example prep info file does not include the R1 suffix, so I'm confused. Your example does include run_file, but I don't see that documented anywhere.

Earlier, @antgonza https://github.com/antgonza mentioned that this might be a bug https://github.com/qiita-spots/qp-target-gene/issues/10. Should I try passing full file names (with R1 suffix) to avoid this bug?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/biocore/qiita/issues/2126#issuecomment-301956784, or mute the thread https://github.com/notifications/unsubscribe-auth/AB69gL0B2avC0M8DFgCwn_7BYJG_eLOtks5r6kiOgaJpZM4NO1uC .

-- Gail Ackermann Knight Lab UCSD glackermann@ucsd.edu ackermag@ucsd.edu

antgonza commented 7 years ago

This is closed via: https://github.com/qiita-spots/qp-target-gene/pull/15. Closing as this is not part of qiita but the qp-target-gene plugin. Please review the solution implemented there.