version: qiime 2024.5
I have been struggling with this error for days:
Matplotlib created a temporary cache directory at /tmp/matplotlib-ffb4e81f because the default path (/home/qiime2/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
There was a problem importing /scratch/rylee650/test_manifest.tsv:
/scratch/rylee650/test_manifest.tsv is not a(n) PairedEndFastqManifestPhred64 file:
Found header on line 1 with the following labels: ['sample-id\tabsolute-filepath\tirection'], expected: ['sample-id', 'absolute-filepath', 'direction']
my import code:
module load qiime2/2024.5
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path /scratch/rylee650/manifest-file.tsv
--output-path demux-paired-end.qza
--input-format PairedEndFastqManifestPhred64
the first few lines of my manifest file using cat -A manifest-file.tsv:
sample-id^Iabsolute-filepath^Idirection$
NX.VH01519_157.001.FLD_ill_097_i7---FLD_ill_0097_i5.V3-RG3-1^I/scratch/rylee650/NX.VH01519_157.001.FLD_ill_097_i7---FLD_ill_0097_i5.V3-RG3-1_R1.fastq.gz^Iforward$
NX.VH01519_157.001.FLD_ill_097_i7---FLD_ill_0097_i5.V3-RG3-1^I/scratch/rylee650/NX.VH01519_157.001.FLD_ill_097_i7---FLD_ill_0097_i5.V3-RG3-1_R2.fastq.gz^Ireverse$
to make the manifest code I used:
echo -e "sample-id\tforward-absolute-filepath\treverse-absolute-filepath" > manifest-file.tsv
for f in *_R1.fastq.gz; do
sample=$(basename "$f" _R1.fastq.gz)
echo -e "$sample\t/scratch/rylee650/${sample}_R1.fastq.gz\t/scratch/rylee650/${sample}_R2.fastq.gz" >> manifest-file.tsv
done
and my samples are for sure phred64:
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIII9II
ive tried so many ways to fix this and it doesn't seem to be working, maybe I am doing it wrong. ive tried rewriting the header using vim as well
my file is ascii and it was edited on a Mac.
please help!!!