Filepath on line 3 and column "forward-absolute-filepath" could not be found error

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1

Hi all,

I am having continuous trouble importing samples in to QIIME. While there are similar posts of this forum regarding this issue, none of them have helped me thus far. I have spellchecked and recopied and pasted, etc and cant find any file path errors.

Here is my error message:

There was a problem importing /local1/workdir1/tw488/CIDA_Sequencing_Runs/ITS_RUNS1_6_allinone/semifinal_manifest.tsv:

/local1/workdir1/tw488/CIDA_Sequencing_Runs/ITS_RUNS1_6_allinone/semifinal_manifest.tsv is not a(n) PairedEndFastqManifestPhred33V2 file:

Filepath on line 3 and column "forward-absolute-filepath" could not be found (/local1/workdir1/tw488/CIDA_Sequencing_Runs/ITS_RUNS1_6_allinone/ITS_0122_A_D12_1_A_R1.fastq.gz) for sample "ITS_0122_A_D12_1_A".

Here is my code:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /local1/workdir1/tw488/CIDA_Sequencing_Runs/ITS_RUNS1_6_allinone/semifinal_manifest.tsv
--input-format PairedEndFastqManifestPhred33V2
--output-path ITS_semifinal.qza

Here are the first few lines of my Manifest, which is a tab separated file:

sample-id forward-absolute-filepath reverse-absolute-filepath
ITS_0122_A_D7_1_AZ /local1/workdir1/tw488/CIDA_Sequencing_Runs/ITS_RUNS1_6_allinone/ITS_0122_A_D7_1_AZ_R1.fastq.gz
/local1/workdir1/tw488/CIDA_Sequencing_Runs/ITS_RUNS1_6_allinone/ITS_0122_A_D7_1_AZ_R2.fastq.gz

ITS_0122_A_D7_3_AZ /local1/workdir1/tw488/CIDA_Sequencing_Runs/ITS_RUNS1_6_allinone/ITS_0122_A_D7_3_AZ_R1.fastq.gz
/local1/workdir1/tw488/CIDA_Sequencing_Runs/ITS_RUNS1_6_allinone/ITS_0122_A_D7_3_AZ_R2.fastq.gz

Please let me know of any other info you might need to help solve this!

Thanks, Tammy

2

Hello @tamardigrade, can you run the command stat /local1/workdir1/tw488/CIDA_Sequencing_Runs/ITS_RUNS1_6_allinone/ITS_0122_A_D12_1_A_R1.fastq.gz and post the results here. Thank you.

3

I did that and got a 'No such file or directory'

I then remade the whole manifest and it worked- unsure of what the problem was but remaking it fixed whatever was wrong. Thank you!

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