Qiime2 import failure

Hello All,
I am using the following command

(qiime2-2021.8) [[email protected] smoking]$ qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path smoking.manifest.txt --output-path paired-end-demux.qza --input-format PairedEndFastqManifestPhred33

I am getting the following message

Also below is a screenshot of my manifest file
Appreciate your support.

File "/data/home/mus4008/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/q2_types/per_sample_sequences/_util.py", line 202, in _validate_paired_end_fastq_manifest_directions
raise ValueError('Forward and reverse reads must be provided '
ValueError: Forward and reverse reads must be provided exactly one time each for each sample. The following samples had forward but not reverse read fastq files: 4882-23_S19_R1_001.fastq.gz, 4882-57_S50_R1_001.fastq.gz, 4882-191_S80_R1_001.fastq.gz, 4882-33_S28_R1_001.fastq.gz, 4882-22_S18_R1_001.fastq.gz, 4882-36_S31_R1_001.fastq.gz, 4882-68_S61_R1_001.fastq.gz, 4882-79_S72_R1_001.fastq.gz, 4882-80_S73_R1_001.fastq.gz, 4882-182_S72_R1_001.fastq.gz, 4882-118_S12_R1_001.fastq.gz, 4882-14_S11_R1_001.fastq.gz, 4882-10_S7_R1_001.fastq.gz, 4882-100_S91_R1_001.fastq.gz, 4882-138_S32_R1_001.fastq.gz, 4882-13_S10_R1_001.fastq.gz, 4882-104_S95_R1_001.fastq.gz, 4882-67_S60_R1_001.fastq.gz, 4882-160_S51_R1_001.fastq.gz, 4882-169_S59_R1_001.fastq.gz, 4882-17_S14_R1_001.fastq.gz, 4882-71_S64_R1_001.fastq.gz, 4882-75_S68_R1_001.fastq.gz, 4882-140_S34_R1_001.fastq.gz, 4882-158_S49_R1_001.fastq.gz, 4882-56_S49_R1_001.fastq.gz, 4882-92_S84_R1_001.fastq.gz, 4882-15_S12_R1_001.fastq.gz, 4882-125_S19_R1_001.fastq.gz, 4882-175_S65_R1_001.fastq.gz, 4882-78_S71_R1_001.fastq.gz, 4882-18_S15_R1_001.fastq.gz, 4882-170_S60_R1_001.fastq.gz, 4882-173_S63_R1_001.fastq.gz, 4882-137_S31_R1_001.fastq.gz, 4882-149_S42_R1_001.fastq.gz, 4882-77_S70_R1_001.fastq.gz, 4882-58_S51_R1_001.fastq.gz, 4882-174_S64_R1_001.fastq.gz, 4882-20_S17_R1_001.fastq.gz, 4882-25_S21_R1_001.fastq.gz, 4882-82_S75_R1_001.fastq.gz, 4882-143_S36_R1_001.fastq.gz, 4882-190_S79_R1_001.fastq.gz, 4882-150_S43_R1_001.fastq.gz, 4882-128_S22_R1_001.fastq.gz, 4882-69_S62_R1_001.fastq.gz, 4882-129_S23_R1_001.fastq.gz, 4882-72_S65_R1_001.fastq.gz, 4882-46_S41_R1_001.fastq.gz, 4882-167_S57_R1_001.fastq.gz, 4882-124_S18_R1_001.fastq.gz, 4882-141_S35_R1_001.fastq.gz, 4882-41_S36_R1_001.fastq.gz, 4882-131_S25_R1_001.fastq.gz, 4882-54_S47_R1_001.fastq.gz, 4882-120_S14_R1_001.fastq.gz, 4882-159_S50_R1_001.fastq.gz, 4882-126_S20_R1_001.fastq.gz, 4882-145_S38_R1_001.fastq.gz, 4882-61_S54_R1_001.fastq.gz, 4882-81_S74_R1_001.fastq.gz, 4882-171_S61_R1_001.fastq.gz, 4882-8_S5_R1_001.fastq.gz, 4882-30_S25_R1_001.fastq.gz, 4882-34_S29_R1_001.fastq.gz, 4882-161_S52_R1_001.fastq.gz, 4882-181_S71_R1_001.fastq.gz, 4882-178_S68_R1_001.fastq.gz, 4882-43_S38_R1_001.fastq.gz, 4882-39_S34_R1_001.fastq.gz, 4882-133_S27_R1_001.fastq.gz, 4882-193_S81_R1_001.fastq.gz, 4882-88_S81_R1_001.fastq.gz, 4882-164_S54_R1_001.fastq.gz, 4882-177_S67_R1_001.fastq.gz, 4882-176_S66_R1_001.fastq.gz, 4882-62_S55_R1_001.fastq.gz, 4882-7_S4_R1_001.fastq.gz, 4882-151_S44_R1_001.fastq.gz, 4882-127_S21_R1_001.fastq.gz, 4882-94_S86_R1_001.fastq.gz, 4882-86_S79_R1_001.fastq.gz, 4882-64_S57_R1_001.fastq.gz, 4882-134_S28_R1_001.fastq.gz, 4882-16_S13_R1_001.fastq.gz, 4882-139_S33_R1_001.fastq.gz, 4882-84_S77_R1_001.fastq.gz, 4882-59_S52_R1_001.fastq.gz, 4882-148_S41_R1_001.fastq.gz, 4882-65_S58_R1_001.fastq.gz, 4882-76_S69_R1_001.fastq.gz, 4882-87_S80_R1_001.fastq.gz, 4882-172_S62_R1_001.fastq.gz, 4882-136_S30_R1_001.fastq.gz, 4882-146_S39_R1_001.fastq.gz, 4882-188_S77_R1_001.fastq.gz, 4882-166_S56_R1_001.fastq.gz, 4882-163_S53_R1_001.fastq.gz, 4882-53_S46_R1_001.fastq.gz, 4882-45_S40_R1_001.fastq.gz, 4882-60_S53_R1_001.fastq.gz, 4882-5_S2_R1_001.fastq.gz, 4882-63_S56_R1_001.fastq.gz, 4882-51_S44_R1_001.fastq.gz, 4882-93_S85_R1_001.fastq.gz, 4882-165_S55_R1_001.fastq.gz, 4882-35_S30_R1_001.fastq.gz, 4882-55_S48_R1_001.fastq.gz, 4882-89_S82_R1_001.fastq.gz, 4882-40_S35_R1_001.fastq.gz, 4882-44_S39_R1_001.fastq.gz, 4882-152_S45_R1_001.fastq.gz, 4882-66_S59_R1_001.fastq.gz, 4882-98_S89_R1_001.fastq.gz, 4882-116_S10_R1_001.fastq.gz, 4882-189_S78_R1_001.fastq.gz, 4882-155_S47_R1_001.fastq.gz, 4882-91_S83_R1_001.fastq.gz, 4882-47_S42_R1_001.fastq.gz, 4882-50_S43_R1_001.fastq.gz, 4882-99_S90_R1_001.fastq.gz, 4882-70_S63_R1_001.fastq.gz, 4882-103_S94_R1_001.fastq.gz, 4882-31_S26_R1_001.fastq.gz, 4882-184_S74_R1_001.fastq.gz, 4882-19_S16_R1_001.fastq.gz, 4882-6_S3_R1_001.fastq.gz, 4882-24_S20_R1_001.fastq.gz, 4882-180_S70_R1_001.fastq.gz, 4882-27_S22_R1_001.fastq.gz, 4882-105_S96_R1_001.fastq.gz, 4882-12_S9_R1_001.fastq.gz, 4882-144_S37_R1_001.fastq.gz, 4882-97_S88_R1_001.fastq.gz, 4882-117_S11_R1_001.fastq.gz, 4882-199_S82_R1_001.fastq.gz, 4882-119_S13_R1_001.fastq.gz, 4882-42_S37_R1_001.fastq.gz, 4882-187_S76_R1_001.fastq.gz, 4882-130_S24_R1_001.fastq.gz, 4882-74_S67_R1_001.fastq.gz, 4882-186_S75_R1_001.fastq.gz, 4882-200_S83_R1_001.fastq.gz, 4882-147_S40_R1_001.fastq.gz, 4882-38_S33_R1_001.fastq.gz, 4882-156_S48_R1_001.fastq.gz, 4882-95_S87_R1_001.fastq.gz, 4882-11_S8_R1_001.fastq.gz, 4882-101_S92_R1_001.fastq.gz, 4882-132_S26_R1_001.fastq.gz, 4882-122_S16_R1_001.fastq.gz, 4882-183_S73_R1_001.fastq.gz, 4882-102_S93_R1_001.fastq.gz, 4882-29_S24_R1_001.fastq.gz, 4882-73_S66_R1_001.fastq.gz, 4882-37_S32_R1_001.fastq.gz, 4882-28_S23_R1_001.fastq.gz, 4882-154_S46_R1_001.fastq.gz, 4882-52_S45_R1_001.fastq.gz, 4882-85_S78_R1_001.fastq.gz, 4882-9_S6_R1_001.fastq.gz, 4882-121_S15_R1_001.fastq.gz, 4882-2_S1_R1_001.fastq.gz, 4882-32_S27_R1_001.fastq.gz, 4882-83_S76_R1_001.fastq.gz, 4882-135_S29_R1_001.fastq.gz, 4882-179_S69_R1_001.fastq.gz, 4882-123_S17_R1_001.fastq.gz, 4882-168_S58_R1_001.fastq.gz

Hi @drmusk,

I think I can see a problem in your metadata file, you using the read fastq file name in the sample id column!
Try to change the manifest file as follow:

sample-id,absolute-filepath,direction
S1,/data/home/mus4008/smoking/4882-2_S1_R1.fastq.gz,forward
S1,/data/home/mus4008/smoking/4882-2_S1_R2.fastq.gz,reverse

Hope it helps
Luca

2 Likes

Thanks @llenzi for pointing out that. I helped. Thanks

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