I am trying to use some data off the ncbi to create some taxonomies but first I am working on the importing step for my fastq data. It is single ended with quality. Here is the command:
iime tools import --type SampleData[SequencesWithQuality] --input-path ./Manifest.csv --output-path single-end-demux.qza --input-format SingleEndFastqManifestPhred33
My Manifest.csv file is like this:
sample-id,absolute-filepath,direction
/home/gomeza/davi2714/Ashok_data/SRP023463/fastq/SRR870254,/home/gomeza/davi2714/Ashok_data/SRP023463/fastq/SRR870254.fastq,forward
/home/gomeza/davi2714/Ashok_data/SRP023463/fastq/SRR870350,/home/gomeza/davi2714/Ashok_data/SRP023463/fastq/SRR870350.fastq,forward
/home/gomeza/davi2714/Ashok_data/SRP023463/fastq/SRR870351,/home/gomeza/davi2714/Ashok_data/SRP023463/fastq/SRR870351.fastq,forward
/home/gomeza/davi2714/Ashok_data/SRP023463/fastq/SRR870352,/home/gomeza/davi2714/Ashok_data/SRP023463/fastq/SRR870352.fastq,forward
/home/gomeza/davi2714/Ashok_data/SRP023463/fastq/SRR870353,/home/gomeza/davi2714/Ashok_data/SRP023463/fastq/SRR870353.fastq,forward
Finally the fastq files themselves look like this generally:
@SRR870404.1 GSXJRPF01EAVZZ length=402
TCAGAACGCACGCTAGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGTTGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCACTCGTCTACCGGAAAATAACCTTTAATCATGCGGACATGTGAACTCATGATGCCATCCTGGATTAATCTTCCTTTCAGAAGGCTGGCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATCAGCCTTAGCAAGCTAAGACCATGCTGCCCCTCGACTTGCATGTGTTAAGCCTGTAGCTAGCGTTCATCCTGAGCCAGGATCAAACTCTGACTGAGCGGGCTGGCAAGGCGCATAG
+SRR870404.1 GSXJRPF01EAVZZ length=402
IIIIIIIIIIIIIIIIIIIIIIIIIIBBBIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIII;;;;;IIIIIIIIIIIIIIIBBB@DDIIIIIIIIIIIIIHHHIEA=AA<A971111126AA;[email protected]:73-005.77?AEEIIIIIBB?;;44;;CCC<<7??IIIIIIIIIIIIIIIIIIIIIIIIIIIIIHEEI;;;;BBEEEEBBA???IIIIIIIIII;;;DIIIIIIIIIIIIII???C???EEEEICBDHGGGIIIIIIIIIIIIIIIIIIIIIIHHHHIIIIIIIIHHHIIIIIICCCCIIIIIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIEEEIIE7779?FEEEDA@@A9422EA@@@777797EIIFI
The error I get is:
There was a problem importing Manifest.csv:
Missing one or more files for SingleLanePerSampleSingleEndFastqDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz
Any ideas on how to fix this? I have checked for any weird spacing in the Manifest.csv file, I have checked if the fastq files are somehow corrupted.
Thanks for the consideration!