Hello - after looking at several help issues on this and correcting those issues in my manifest file I am still getting the error that my file is not a manifest phred33 (or phred64 file).
(qiime2-2017.10) wsb255bioimac27:Fink_fermenter_Exp3 mel_local$ qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path AD_exp3_Arc_manifest-pe.csv --output-path AD_exp3_Arc_pe-demux.qza --source-format PairedEndFastqManifestPhred33
There was a problem importing AD_exp3_Arc_manifest-pe.csv:
AD_exp3_Arc_manifest-pe.csv is not a(n) PairedEndFastqManifestPhred33 file
I created the file in excel (grrrr). It resulted in extra comma's which I removed. I then found a spelling error in the headers. Otherwise for the life of me I cannot seem to find what is preventing the import.
I did :set list to see if there were hidden characters to remove and I only saw the end-line character $
I also tried awking out my columns from the csv file into a different file to make sure only the 3 columns were included and that file didn't work either.
Originally I had periods in my sample-id names so I changed those to underscores. Checked the file path which is correct. The only thing is there are more files than what I am loading up in that directory but I didn't think that would/should matter.
(qiime2-2017.10) wsb255bioimac27:Fink_fermenter_Exp3 mel_local$ ls Fink_Project_008/
Analysis F1_41_5_Arc_S50_R2_001.fastq.gz F2_0_5_Pro_S135_R2_001.fastq.gz F2_42_V4_S40_R2_001.fastq.gz
BLANK_Arc_G06_S90_R1_001.fastq.gz F1_41_5_Pro_S98_R1_001.fastq.gz F2_0_5_V4_S39_R1_001.fastq.gz F2_43_5_Arc_S53_R1_001.fastq.gz
BLANK_Arc_G06_S90_R2_001.fastq.gz F1_41_5_Pro_S98_R2_001.fastq.gz F2_0_5_V4_S39_R2_001.fastq.gz F2_43_5_Arc_S53_R2_001.fastq.gz
BLANK_Arc_H06_S96_R1_001.fastq.gz F1_41_5_V4_S2_R1_001.fastq.gz F2_0_Arc_S81_R1_001.fastq.gz F2_43_5_Pro_S101_R1_001.fastq.gz
BLANK_Arc_H06_S96_R2_001.fastq.gz F1_41_5_V4_S2_R2_001.fastq.gz F2_0_Arc_S81_R2_001.fastq.gz F2_43_5_Pro_S101_R2_001.fastq.gz
BLANK_Pro_G06_S138_R1_001.fastq.gz F1_42_5_Arc_S62_R1_001.fastq.gz F2_0_Pro_S129_R1_001.fastq.gz F2_43_5_V4_S5_R1_001.fastq.gz
BLANK_Pro_G06_S138_R2_001.fastq.gz F1_42_5_Arc_S62_R2_001.fastq.gz F2_0_Pro_S129_R2_001.fastq.gz F2_43_5_V4_S5_R2_001.fastq.gz
BLANK_Pro_H06_S144_R1_001.fastq.gz F1_42_5_Pro_S110_R1_001.fastq.gz F2_0_V4_S33_R1_001.fastq.gz F2_45_5_Arc_S59_R1_001.fastq.gz
BLANK_Pro_H06_S144_R2_001.fastq.gz F1_42_5_Pro_S110_R2_001.fastq.gz F2_0_V4_S33_R2_001.fastq.gz F2_45_5_Arc_S59_R2_001.fastq.gz
BLANK_V4_G06_S42_R1_001.fastq.gz F1_42_5_V4_S14_R1_001.fastq.gz F2_101_5_Arc_S89_R1_001.fastq.gz F2_45_5_Pro_S107_R1_001.fastq.gz
BLANK_V4_G06_S42_R2_001.fastq.gz F1_42_5_V4_S14_R2_001.fastq.gz F2_101_5_Arc_S89_R2_001.fastq.gz F2_45_5_Pro_S107_R2_001.fastq.gz
BLANK_V4_H06_S48_R1_001.fastq.gz F1_42_Arc_S56_R1_001.fastq.gz F2_101_5_Pro_S137_R1_001.fastq.gz F2_45_5_V4_S11_R1_001.fastq.gz
BLANK_V4_H06_S48_R2_001.fastq.gz F1_42_Arc_S56_R2_001.fastq.gz F2_101_5_Pro_S137_R2_001.fastq.gz F2_45_5_V4_S11_R2_001.fastq.gz
F1_0_5_Arc_S55_R1_001.fastq.gz F1_42_Pro_S104_R1_001.fastq.gz F2_101_5_V4_S41_R1_001.fastq.gz F2_49_5_Arc_S65_R1_001.fastq.gz
F1_0_5_Arc_S55_R2_001.fastq.gz F1_42_Pro_S104_R2_001.fastq.gz F2_101_5_V4_S41_R2_001.fastq.gz F2_49_5_Arc_S65_R2_001.fastq.gz
F1_0_5_Pro_S103_R1_001.fastq.gz F1_42_V4_S8_R1_001.fastq.gz F2_128_5_Arc_S95_R1_001.fastq.gz F2_49_5_Pro_S113_R1_001.fastq.gz
F1_0_5_Pro_S103_R2_001.fastq.gz F1_42_V4_S8_R2_001.fastq.gz F2_128_5_Arc_S95_R2_001.fastq.gz F2_49_5_Pro_S113_R2_001.fastq.gz
F1_0_5_V4_S7_R1_001.fastq.gz F1_43_5_Arc_S68_R1_001.fastq.gz F2_128_5_Pro_S143_R1_001.fastq.gz F2_49_5_V4_S17_R1_001.fastq.gz
F1_0_5_V4_S7_R2_001.fastq.gz F1_43_5_Arc_S68_R2_001.fastq.gz F2_128_5_Pro_S143_R2_001.fastq.gz F2_49_5_V4_S17_R2_001.fastq.gz
F1_0_Arc_S49_R1_001.fastq.gz F1_43_5_Pro_S116_R1_001.fastq.gz F2_128_5_V4_S47_R1_001.fastq.gz F2_4_Arc_S58_R1_001.fastq.gz
F1_0_Arc_S49_R2_001.fastq.gz F1_43_5_Pro_S116_R2_001.fastq.gz F2_128_5_V4_S47_R2_001.fastq.gz F2_4_Arc_S58_R2_001.fastq.gz
F1_0_Pro_S97_R1_001.fastq.gz F1_43_5_V4_S20_R1_001.fastq.gz F2_155_5_Arc_S54_R1_001.fastq.gz F2_4_Pro_S106_R1_001.fastq.gz
F1_0_Pro_S97_R2_001.fastq.gz F1_43_5_V4_S20_R2_001.fastq.gz F2_155_5_Arc_S54_R2_001.fastq.gz F2_4_Pro_S106_R2_001.fastq.gz
F1_0_V4_S1_R1_001.fastq.gz F1_45_5_Arc_S74_R1_001.fastq.gz F2_155_5_Pro_S102_R1_001.fastq.gz F2_4_V4_S10_R1_001.fastq.gz
F1_0_V4_S1_R2_001.fastq.gz F1_45_5_Arc_S74_R2_001.fastq.gz F2_155_5_Pro_S102_R2_001.fastq.gz F2_4_V4_S10_R2_001.fastq.gz
F1_101_5_Arc_S57_R1_001.fastq.gz F1_45_5_Pro_S122_R1_001.fastq.gz F2_155_5_V4_S6_R1_001.fastq.gz F2_57_5_Arc_S71_R1_001.fastq.gz
F1_101_5_Arc_S57_R2_001.fastq.gz F1_45_5_Pro_S122_R2_001.fastq.gz F2_155_5_V4_S6_R2_001.fastq.gz F2_57_5_Arc_S71_R2_001.fastq.gz
F1_101_5_Pro_S105_R1_001.fastq.gz F1_45_5_V4_S26_R1_001.fastq.gz F2_16_Arc_S70_R1_001.fastq.gz F2_57_5_Pro_S119_R1_001.fastq.gz
F1_101_5_Pro_S105_R2_001.fastq.gz F1_45_5_V4_S26_R2_001.fastq.gz F2_16_Arc_S70_R2_001.fastq.gz F2_57_5_Pro_S119_R2_001.fastq.gz
F1_101_5_V4_S9_R1_001.fastq.gz F1_49_5_Arc_S80_R1_001.fastq.gz F2_16_Pro_S118_R1_001.fastq.gz F2_57_5_V4_S23_R1_001.fastq.gz
F1_101_5_V4_S9_R2_001.fastq.gz F1_49_5_Arc_S80_R2_001.fastq.gz F2_16_Pro_S118_R2_001.fastq.gz F2_57_5_V4_S23_R2_001.fastq.gz
F1_128_5_Arc_S63_R1_001.fastq.gz F1_49_5_Pro_S128_R1_001.fastq.gz F2_16_V4_S22_R1_001.fastq.gz F2_65_5_Arc_S77_R1_001.fastq.gz
F1_128_5_Arc_S63_R2_001.fastq.gz F1_49_5_Pro_S128_R2_001.fastq.gz F2_16_V4_S22_R2_001.fastq.gz F2_65_5_Arc_S77_R2_001.fastq.gz
F1_128_5_Pro_S111_R1_001.fastq.gz F1_49_5_V4_S32_R1_001.fastq.gz F2_182_5_Arc_S60_R1_001.fastq.gz F2_65_5_Pro_S125_R1_001.fastq.gz
F1_128_5_Pro_S111_R2_001.fastq.gz F1_49_5_V4_S32_R2_001.fastq.gz F2_182_5_Arc_S60_R2_001.fastq.gz F2_65_5_Pro_S125_R2_001.fastq.gz
F1_128_5_V4_S15_R1_001.fastq.gz F1_4_Arc_S73_R1_001.fastq.gz F2_182_5_Pro_S108_R1_001.fastq.gz F2_65_5_V4_S29_R1_001.fastq.gz
F1_128_5_V4_S15_R2_001.fastq.gz F1_4_Arc_S73_R2_001.fastq.gz F2_182_5_Pro_S108_R2_001.fastq.gz F2_65_5_V4_S29_R2_001.fastq.gz
F1_155_5_Arc_S69_R1_001.fastq.gz F1_4_Pro_S121_R1_001.fastq.gz F2_182_5_V4_S12_R1_001.fastq.gz F2_89_5_Arc_S83_R1_001.fastq.gz
F1_155_5_Arc_S69_R2_001.fastq.gz F1_4_Pro_S121_R2_001.fastq.gz F2_182_5_V4_S12_R2_001.fastq.gz F2_89_5_Arc_S83_R2_001.fastq.gz
F1_155_5_Pro_S117_R1_001.fastq.gz F1_4_V4_S25_R1_001.fastq.gz F2_1_Arc_S93_R1_001.fastq.gz F2_89_5_Pro_S131_R1_001.fastq.gz
F1_155_5_Pro_S117_R2_001.fastq.gz F1_4_V4_S25_R2_001.fastq.gz F2_1_Arc_S93_R2_001.fastq.gz F2_89_5_Pro_S131_R2_001.fastq.gz
F1_155_5_V4_S21_R1_001.fastq.gz F1_57_5_Arc_S86_R1_001.fastq.gz F2_1_Pro_S141_R1_001.fastq.gz F2_89_5_V4_S35_R1_001.fastq.gz
F1_155_5_V4_S21_R2_001.fastq.gz F1_57_5_Arc_S86_R2_001.fastq.gz F2_1_Pro_S141_R2_001.fastq.gz F2_89_5_V4_S35_R2_001.fastq.gz
F1_16_Arc_S85_R1_001.fastq.gz F1_57_5_Pro_S134_R1_001.fastq.gz F2_1_V4_S45_R1_001.fastq.gz F2_8_Arc_S64_R1_001.fastq.gz
F1_16_Arc_S85_R2_001.fastq.gz F1_57_5_Pro_S134_R2_001.fastq.gz F2_1_V4_S45_R2_001.fastq.gz F2_8_Arc_S64_R2_001.fastq.gz
F1_16_Pro_S133_R1_001.fastq.gz F1_57_5_V4_S38_R1_001.fastq.gz F2_24_Arc_S76_R1_001.fastq.gz F2_8_Pro_S112_R1_001.fastq.gz
F1_16_Pro_S133_R2_001.fastq.gz F1_57_5_V4_S38_R2_001.fastq.gz F2_24_Arc_S76_R2_001.fastq.gz F2_8_Pro_S112_R2_001.fastq.gz
F1_16_V4_S37_R1_001.fastq.gz F1_65_5_Arc_S92_R1_001.fastq.gz F2_24_Pro_S124_R1_001.fastq.gz F2_8_V4_S16_R1_001.fastq.gz
F1_16_V4_S37_R2_001.fastq.gz F1_65_5_Arc_S92_R2_001.fastq.gz F2_24_Pro_S124_R2_001.fastq.gz F2_8_V4_S16_R2_001.fastq.gz
F1_182_5_Arc_S75_R1_001.fastq.gz F1_65_5_Pro_S140_R1_001.fastq.gz F2_24_V4_S28_R1_001.fastq.gz F2_W_Arc_S84_R1_001.fastq.gz
F1_182_5_Arc_S75_R2_001.fastq.gz F1_65_5_Pro_S140_R2_001.fastq.gz F2_24_V4_S28_R2_001.fastq.gz F2_W_Arc_S84_R2_001.fastq.gz
F1_182_5_Pro_S123_R1_001.fastq.gz F1_65_5_V4_S44_R1_001.fastq.gz F2_2_Arc_S52_R1_001.fastq.gz F2_W_Pro_S132_R1_001.fastq.gz
F1_182_5_Pro_S123_R2_001.fastq.gz F1_65_5_V4_S44_R2_001.fastq.gz F2_2_Arc_S52_R2_001.fastq.gz F2_W_Pro_S132_R2_001.fastq.gz
F1_182_5_V4_S27_R1_001.fastq.gz F1_89_5_Arc_S51_R1_001.fastq.gz F2_2_Pro_S100_R1_001.fastq.gz F2_W_V4_S36_R1_001.fastq.gz
F1_182_5_V4_S27_R2_001.fastq.gz F1_89_5_Arc_S51_R2_001.fastq.gz F2_2_Pro_S100_R2_001.fastq.gz F2_W_V4_S36_R2_001.fastq.gz
F1_1_Arc_S61_R1_001.fastq.gz F1_89_5_Pro_S99_R1_001.fastq.gz F2_2_V4_S4_R1_001.fastq.gz FD1_Arc_S66_R1_001.fastq.gz
F1_1_Arc_S61_R2_001.fastq.gz F1_89_5_Pro_S99_R2_001.fastq.gz F2_2_V4_S4_R2_001.fastq.gz FD1_Arc_S66_R2_001.fastq.gz
F1_1_Pro_S109_R1_001.fastq.gz F1_89_5_V4_S3_R1_001.fastq.gz F2_41_5_Arc_S82_R1_001.fastq.gz FD1_Pro_S114_R1_001.fastq.gz
F1_1_Pro_S109_R2_001.fastq.gz F1_89_5_V4_S3_R2_001.fastq.gz F2_41_5_Arc_S82_R2_001.fastq.gz FD1_Pro_S114_R2_001.fastq.gz
F1_1_V4_S13_R1_001.fastq.gz F1_8_Arc_S79_R1_001.fastq.gz F2_41_5_Pro_S130_R1_001.fastq.gz FD1_V4_S18_R1_001.fastq.gz
F1_1_V4_S13_R2_001.fastq.gz F1_8_Arc_S79_R2_001.fastq.gz F2_41_5_Pro_S130_R2_001.fastq.gz FD1_V4_S18_R2_001.fastq.gz
F1_24_Arc_S91_R1_001.fastq.gz F1_8_Pro_S127_R1_001.fastq.gz F2_41_5_V4_S34_R1_001.fastq.gz M1_Arc_S72_R1_001.fastq.gz
F1_24_Arc_S91_R2_001.fastq.gz F1_8_Pro_S127_R2_001.fastq.gz F2_41_5_V4_S34_R2_001.fastq.gz M1_Arc_S72_R2_001.fastq.gz
F1_24_Pro_S139_R1_001.fastq.gz F1_8_V4_S31_R1_001.fastq.gz F2_42_5_Arc_S94_R1_001.fastq.gz M1_Pro_S120_R1_001.fastq.gz
F1_24_Pro_S139_R2_001.fastq.gz F1_8_V4_S31_R2_001.fastq.gz F2_42_5_Arc_S94_R2_001.fastq.gz M1_Pro_S120_R2_001.fastq.gz
F1_24_V4_S43_R1_001.fastq.gz F1_W_Arc_S78_R1_001.fastq.gz F2_42_5_Pro_S142_R1_001.fastq.gz M1_V4_S24_R1_001.fastq.gz
F1_24_V4_S43_R2_001.fastq.gz F1_W_Arc_S78_R2_001.fastq.gz F2_42_5_Pro_S142_R2_001.fastq.gz M1_V4_S24_R2_001.fastq.gz
F1_2_Arc_S67_R1_001.fastq.gz F1_W_Pro_S126_R1_001.fastq.gz F2_42_5_V4_S46_R1_001.fastq.gz index.html?C=M;O=A
F1_2_Arc_S67_R2_001.fastq.gz F1_W_Pro_S126_R2_001.fastq.gz F2_42_5_V4_S46_R2_001.fastq.gz index.html?C=M;O=D
F1_2_Pro_S115_R1_001.fastq.gz F1_W_V4_S30_R1_001.fastq.gz F2_42_Arc_S88_R1_001.fastq.gz index.html?C=N;O=A
F1_2_Pro_S115_R2_001.fastq.gz F1_W_V4_S30_R2_001.fastq.gz F2_42_Arc_S88_R2_001.fastq.gz index.html?C=N;O=D
F1_2_V4_S19_R1_001.fastq.gz F2_0_5_Arc_S87_R1_001.fastq.gz F2_42_Pro_S136_R1_001.fastq.gz index.html?C=S;O=A
F1_2_V4_S19_R2_001.fastq.gz F2_0_5_Arc_S87_R2_001.fastq.gz F2_42_Pro_S136_R2_001.fastq.gz index.html?C=S;O=D
F1_41_5_Arc_S50_R1_001.fastq.gz F2_0_5_Pro_S135_R1_001.fastq.gz F2_42_V4_S40_R1_001.fastq.gz md5.txt
(qiime2-2017.10) wsb255bioimac27:Fink_fermenter_Exp3 mel_local$ head AD_exp3_Arc_manifest-pe.csv
sample-id,absolute-filepath,direction
BLANK1,/Users/mel_local/Analysis/qiime/Fink_fermenter_Exp3/Fink_Project_008/BLANK_Arc_G06_S90_R1_001.fastq.gz,forward
BLANK1,/Users/mel_local/Analysis/qiime/Fink_fermenter_Exp3/Fink_Project_008/BLANK_Arc_G06_S90_R2_001.fastq.gz,reverse
BLANK2,/Users/mel_local/Analysis/qiime/Fink_fermenter_Exp3/Fink_Project_008/BLANK_Arc_H06_S96_R1_001.fastq.gz,forward
BLANK2,/Users/mel_local/Analysis/qiime/Fink_fermenter_Exp3/Fink_Project_008/BLANK_Arc_H06_S96_R2_001.fastq.gz,reverse
F1_0_5,/Users/mel_local/Analysis/qiime/Fink_fermenter_Exp3/Fink_Project_008/F1_0_5_Arc_S55_R1_001.fastq.gz,forward
F1_0_5,/Users/mel_local/Analysis/qiime/Fink_fermenter_Exp3/Fink_Project_008/F1_0_5_Arc_S55_R2_001.fastq.gz,reverse
F1_0,/Users/mel_local/Analysis/qiime/Fink_fermenter_Exp3/Fink_Project_008/F1_0_Arc_S49_R1_001.fastq.gz,forward
F1_0,/Users/mel_local/Analysis/qiime/Fink_fermenter_Exp3/Fink_Project_008/F1_0_Arc_S49_R2_001.fastq.gz,reverse
F1_1,/Users/mel_local/Analysis/qiime/Fink_fermenter_Exp3/Fink_Project_008/F1_1_Arc_S61_R1_001.fastq.gz,forward
Still no luck getting an import. I must be missing something...I need another pair of eyes. I have included the manifest CSV.
Thank you!AD_exp3_Arc_manifest-pe.csv (10.9 KB)