Hi,
I am new to QIIME. I have a dataset downloaded from SRA, where each folder for each sample. No barcode file. So is the data demultiplexed?
This is how the sequences in each file look like,
@SRR9680011.1.1 length=441
TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACACGCAGATGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAAGCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTGGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCGGGGAACTGCATCTGATACGGGAAAGCTGGAGTCTCGTAGAGGGGGGTAGAATGCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCT
+SRR9680011.1.1 length=441
EFFFGG7F@EFFCAGFFFG8FFGGGD7DFCGGGFGDEGFDFFGGG7FFGFFGGGGCFGFG8EFGFCGEFGGGGFGFEDFGGEFFFGGGCFBF=CE<F+4BFADC9FF,C<FFA<F<BDGFF==9DFFB+3>,>3CCGG,3,@FDEFFCGD@1@E$F:FEFEEFFGGFGGDDCEC@EGC>;3B>=FFGGGGEFGGGCC#@EE)EC80A:??DCE/C>8>+:55CG;=CDEF>&C#CCFGFF@F=F7EFDB,?+<7CC8?F?>9(E’F<76GGDGGFF9,?FDGBEFB,@,@DD<@,<D@++77FF8C7C+=DEGGDGFB4,F?GGFGGEGGGGFCFGGEBGGFFE;A9,A=CCFFE?DC=F@6:CFC<FGGEECCFFF7FCF@C6<C9FFFFCGGGFBE@GEEGGGGGGEF7F,FF@FFCFEGGGFFGFF,GGGGCCCCC
@SRR9680011.2.1 length=441
TGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCT
+SRR9680011.2.1 length=441
The library layout is shown as SINGLE
I imported just 2 files coresponding to 2 samples using the command
qiime tools import --type ‘SampleData[SequencesWithQuality]’ --input-path manifestFile --output-path single-end-demux.qza --input-format SingleEndFastqManifestPhred33
my manifest file is
sample-id,absolute-filepath,direction
SRR9679959,/Users/syama/Downloads/sequences/SRR9679959.fastq,forward
SRR9680011,/Users/syama/Downloads/sequences/SRR9680011.fastq,forward
It successfully run and I got single-end-demux.qza
But when I tried demux summary using
qiime demux summarize \
–i-data single-end-demux.qza
–o-visualization demux.qzv
I got the error Plugin error from demux:
’NoneType’ object has no attribute 'strip’
Debug info has been saved to /var/folders/hr/9vcxtv2961bgx43wk4sqww3m0000gn/T/qiime2-q2cli-err-pdlqug93.log
I could not find the above said log file also.
While I open single-end-demux.qza using vi editor it is like,
P??P?G?2c150c2ea-4422-40b4-b3d0-c3d81d9fd4b9/metadata.yaml%˱? ?ᝧ?H1??֩C???- P>???P??PlÃ?4;2c150c2ea-4422-40b4-b3d0-c3d81d9fd4b9/checksums.md5???jA
???k?[?jsp?۰Ԓ:,???<}fɆx???R_?e?fHñ??v?Q?;Oӗ???nS??%lR?R??b-y?D??X?u??w}???z)?h(?y`H?R?4??W??n>^??o???"T??dV??J?Aq??w;?,Rd???;?W?}]??lx??
b,?[ࠜ?uf??>??$???"
CSf?4y???9?O?S???G=Z???=?@@??)?7<p?5?^@vXt9<???+??? ?[ư5???{cvNE??/P??ͳ???(,c150c2ea-4422-40b4-b3d0-c3d81d9fd4b9/VERSION
???uU0?J,J??,K?R0?J+J?M-?/ʶR020??34?3?P??P?G?=c150c2ea-4422-40b4-b3d0-c3d81d9fd4b9/provenance/metadata.yaml%˱? >???P??PZ@???7G???Lׄ#??*? ?1ZK???A%]???+??q
=c150c2ea-4422-40b4-b3d0-c3d81d9fd4b9/provenance/citations.bib}VKv??s??ز%???BQ??L2??]?r b?1>?(ۇ?2???K5???M6Q?h???;Y/?J|[X?œ???_???^o??^g???+c?ߊo’F
are the fastq files properly imported?
I am using Mac Os Catalina version 10.15.4 (19E287)
qiime2-2019.10,
R version 3.5.1
It would be great if someone has the answer.
Tnanks