Hi, I am new to qiime2, I recently received the demultiplexed reads from a Hiseq illumina company that looks like: AOAM-1-sample1_trimmedPR_join.fastq.gz per sample. I have so far 210 files like that. I used this command for import in my HPC cluster: qiime tools import --type SampleData[JoinedS…

Hey there @Hajar ! [image] Hajar: I am new to qiime2, Welcome! :house: [image] Hajar: My question is that do I need to prepare Manifest file or not? Yes. Otherwise, you could rename your files to match the spec , but that would be a lot more work, IMO. [image] Hajar: Is there a wa…

Thanks for your reply, Actually, as you mentioned,I prepared the manifest file but did not work: Below the command line used with the error got: (/mnt/beegfs/home/eh309/qiime2) [eh309@gm-hpc-login-01 HWL-trimmed]$ qiime tools import \ --type 'SampleData[PairedEndSequencesWithQuality]' --input…

Hey @Hajar ! [image] Hajar: I spend three weeks only on importing this :(. Yikes! We are always here to help... [image] Hajar: /mnt/beegfs/scratch/eh309/rawdata/sampletesting/HWL-trimmed is not a file. The --input-path flag should point to your manifest.csv: qiime tools import \ --…

Hey Matthew, Many thanks for you reply, please see below the suggested command and the error got: (/mnt/beegfs/home/eh309/qiime2) [eh309@gm-hpc-login-01 HWL-trimmed] pwd /mnt/beegfs/scratch/eh309/rawdata/sampletesting/HWL-trimmed (/mnt/beegfs/home/eh309/qiime2) [eh309@gm-hpc-login-01 HWL-trimmed] …

[image] Hajar: /mnt/beegfs/scratch/eh309/rawdata/sampletesting/HWL-trimmed/to/manifest.csv is this the path to your manifest file? The error indicates that there is no file found at that location, which makes sense, since it looks like you copied-and-pasted some of my boilerplate from above (/…

glad to let you know that the manifest worked for me the command used: qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /mnt/beegfs/scratch/eh309/rawdata/sampletesting/HWL-trimmed/manifest.csv --output-path single-end-demux.qza --source-format PairedEndFas…

[image] Hajar: import as cassava This format is just a convenience format for importing files that meet a specific naming convention , the data isn't implicated at all, which means that there is no difference in the final result when using CasavaOneEightSingleLanePerSampleDirFmt or a manifest…

thanks a lot for all your efforts

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