Manifest file error on import

(Ariangela Davis) #1

I am trying to import sequences as manifest format.
I am running Qiime 2 version 2019.1, installed with conda.

This is the code I ran:

qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path crn_manifest.csv
–output-path paired-end-demux.qza
–input-format PairedEndFastqManifestPhred33

This is the error I got:
Traceback (most recent call last):
File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/tools.py”, line 146, in import_data
view_type=input_format)
File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 240, in import_data
return cls.from_view(type, view, view_type, provenance_capture)
File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 265, in _from_view
result = transformation(view)
File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/core/transform.py”, line 70, in transformation
new_view = transformer(view)
File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 338, in _8
single_end=False)
File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 268, in _fastq_manifest_helper
absolute=True)
File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 158, in _parse_and_validate_manifest
_validate_paired_end_fastq_manifest_directions(manifest)
File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 211, in _validate_paired_end_fastq_manifest_directions
‘“reverse”, but observed: %s’ % direction)
ValueError: Directions can only be “forward” or “reverse”, but observed: reverse

An unexpected error has occurred:

Directions can only be “forward” or “reverse”, but observed: reverse

See above for debug info.

I know that whitespace used to cause this issue but I have checked for that (I think).
Manifest file attached.
crn_manifest.csv (25.3 KB)

Thanks for your help

(Mehrbod Estaki) #2

Hi @Ariangela_Davis,
It looks as though one of your cells has a an extra space at the end of ‘reverse’ which is being interpreted as a 3rd, unrecognized word.
Specifically, your sample N2_7. Just delete the extra space at the end of ‘reverse’ there and you should be good to go!

N2_7,/Users/dariange/col-crn/COL_CRN_ALL/026146_N2-7_S65_R2_filtered.fastq.gz,reverse^I$

1 Like
(Ariangela Davis) #4

Thank you! That seems to have worked for import, but now I am getting a DADA2 error about mismatched forward and reverse reads, and I do not know how to identify which sample it is in. Here is the relevant script snippets. Here is the code I ran:

qiime dada2 denoise-paired
–i-demultiplexed-seqs paired-end-demux.qza
–p-trim-left-f 12
–p-trim-left-r 12
–p-trunc-len-f 240
–p-trunc-len-r 240
–o-table table.qza
–o-representative-sequences rep-seqs.qza
–o-denoising-stats denoising-stats.qza

Here is the plugin error:

Plugin error from dada2:

An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

Debug info has been saved to /var/folders/87/7xcy8bfn3_1ffmdy7g5fsg550wznls/T/qiime2-q2cli-err-l9_tosxy.log

And here is the error from the temp file:

Command: run_dada_paired.R /var/folders/87/7xcy8bfn3_1ffmdy7g5fsg550wznls/T/tmpku8h9rol/forward /var/folders/87/7xcy8bfn3_1ffmdy7g5fsg550wz
nls/T/tmpku8h9rol/reverse /var/folders/87/7xcy8bfn3_1ffmdy7g5fsg550wznls/T/tmpku8h9rol/output.tsv.biom /var/folders/87/7xcy8bfn3_1ffmdy7g5f
sg550wznls/T/tmpku8h9rol/track.tsv /var/folders/87/7xcy8bfn3_1ffmdy7g5fsg550wznls/T/tmpku8h9rol/filt_f /var/folders/87/7xcy8bfn3_1ffmdy7g5f
sg550wznls/T/tmpku8h9rol/filt_r 240 240 12 12 2.0 2 consensus 1.0 1 1000000

R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0

  1. Filtering Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
    Mismatched forward and reverse sequence files: 85514, 69875.
    Execution halted
    Traceback (most recent call last):
    File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 231, in denoise_paired
    run_commands([cmd])
    File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
    subprocess.run(cmd, check=True)
    File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/subprocess.py”, line 418, in run
    output=stdout, stderr=stderr)
    subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/var/folders/87/7xcy8bfn3_1ffmdy7g5fsg550wznls/T/tmpku8h9rol/forward’, ‘/var
    /folders/87/7xcy8bfn3_1ffmdy7g5fsg550wznls/T/tmpku8h9rol/reverse’, ‘/var/folders/87/7xcy8bfn3_1ffmdy7g5fsg550wznls/T/tmpku8h9rol/output.tsv
    .biom’, ‘/var/folders/87/7xcy8bfn3_1ffmdy7g5fsg550wznls/T/tmpku8h9rol/track.tsv’, ‘/var/folders/87/7xcy8bfn3_1ffmdy7g5fsg550wznls/T/tmpku8h
    9rol/filt_f’, ‘/var
    /folders/87/7xcy8bfn3_1ffmdy7g5fsg550wznls/T/tmpku8h9rol/filt_r’, ‘240’, ‘240’, ‘12’, ‘12’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “</Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-442>”, line 2, in denoise_paired
File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable(**view_args)
File “/Users/dariange/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 246, in denoise_paired
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

(Matthew Ryan Dillon) #5

Double check your manifest, you likely put reads from two different samples into the same “sample” ID. I just took a quick look and noticed, for example, that you don’t have a reverse reads for many of your samples.

(Ariangela Davis) #6

It does appear that way because they are not in order, but from my last check I did not see a non-matched pair. I will check over it again though.

(Matthew Ryan Dillon) #7

B1_5 does not have reverse reads.

(Ariangela Davis) #8

Oh that threw an error at import. I should have updated the manifest file when I asked a new question. My apologies. Here is the current one. crn_manifest.csv (25.3 KB)

(Matthew Ryan Dillon) #9

Thanks!

Can you run the following command?

qiime tools validate paired-end-demux.qza
(Ariangela Davis) #10

Result paired-end-demux.qza appears to be valid at level=max.

(Ariangela Davis) #11

Aha! In sample C2-1 it looks like I have the reverse reads labeled as both the forward and reverse. That would match the error I am getting correct? If so, I will run it again after I correct that line.

2 Likes
(Ariangela Davis) #12

Fixed the C2_1 sample, but I am still getting the same error. crn_manifest.csv (25.3 KB)

(Matthew Ryan Dillon) #13

Cool, so let’s assume your manifest is good to go — all of your samples have the correct forward and reverse file. The error you reported above is that one sample has very different read counts in the forward versus the reverse files — the read counts should be identical. Unfortunately, the error message from DADA2 isn’t very helpful here, it would be ideal if it told us which sample was the culprit. One way to check the read counts:

qiime tools export --input-path paired-end-demux.qza --output-path import-check
cd import-check
for f in *.fastq.gz; do r=$(( $(zcat -f < $f | wc -l | tr -d '[:space:]') / 4 )); echo $r $f; done

Then, paste the results here and we can take a look. Thanks!

1 Like
(Ariangela Davis) #14

41042 B1_10_18_L001_R1_001.fastq.gz

41042 B1_10_27_L001_R2_001.fastq.gz

164485 B1_11_19_L001_R1_001.fastq.gz

164485 B1_11_28_L001_R2_001.fastq.gz

74836 B1_12_20_L001_R1_001.fastq.gz

74836 B1_12_29_L001_R2_001.fastq.gz

16650 B1_13_21_L001_R1_001.fastq.gz

16650 B1_13_30_L001_R2_001.fastq.gz

73135 B1_14_22_L001_R1_001.fastq.gz

73135 B1_14_31_L001_R2_001.fastq.gz

10314 B1_15_23_L001_R1_001.fastq.gz

10314 B1_15_32_L001_R2_001.fastq.gz

49814 B1_16_24_L001_R1_001.fastq.gz

49814 B1_16_33_L001_R2_001.fastq.gz

55985 B1_18_25_L001_R1_001.fastq.gz

55985 B1_18_34_L001_R2_001.fastq.gz

47051 B1_19_26_L001_R1_001.fastq.gz

47051 B1_19_35_L001_R2_001.fastq.gz

119688 B1_1_0_L001_R1_001.fastq.gz

119688 B1_1_1_L001_R2_001.fastq.gz

33867 B1_20_36_L001_R1_001.fastq.gz

33867 B1_20_37_L001_R2_001.fastq.gz

3053 B1_2_2_L001_R1_001.fastq.gz

3053 B1_2_3_L001_R2_001.fastq.gz

53263 B1_3_4_L001_R1_001.fastq.gz

53263 B1_3_5_L001_R2_001.fastq.gz

53092 B1_4_6_L001_R1_001.fastq.gz

53092 B1_4_7_L001_R2_001.fastq.gz

52991 B1_5_8_L001_R1_001.fastq.gz

52991 B1_5_9_L001_R2_001.fastq.gz

71395 B1_6_10_L001_R1_001.fastq.gz

71395 B1_6_11_L001_R2_001.fastq.gz

5989 B1_7_12_L001_R1_001.fastq.gz

5989 B1_7_13_L001_R2_001.fastq.gz

86488 B1_8_14_L001_R1_001.fastq.gz

86488 B1_8_15_L001_R2_001.fastq.gz

58562 B1_9_16_L001_R1_001.fastq.gz

58562 B1_9_17_L001_R2_001.fastq.gz

117447 B2_10_56_L001_R1_001.fastq.gz

117447 B2_10_57_L001_R2_001.fastq.gz

19820 B2_11_58_L001_R1_001.fastq.gz

19820 B2_11_59_L001_R2_001.fastq.gz

14404 B2_12_60_L001_R1_001.fastq.gz

14404 B2_12_61_L001_R2_001.fastq.gz

218249 B2_13_62_L001_R1_001.fastq.gz

218249 B2_13_63_L001_R2_001.fastq.gz

94916 B2_15_64_L001_R1_001.fastq.gz

94916 B2_15_65_L001_R2_001.fastq.gz

102627 B2_16_66_L001_R1_001.fastq.gz

102627 B2_16_67_L001_R2_001.fastq.gz

93440 B2_17_68_L001_R1_001.fastq.gz

93440 B2_17_69_L001_R2_001.fastq.gz

78932 B2_18_70_L001_R1_001.fastq.gz

78932 B2_18_71_L001_R2_001.fastq.gz

75680 B2_19_72_L001_R1_001.fastq.gz

75680 B2_19_73_L001_R2_001.fastq.gz

37613 B2_1_38_L001_R1_001.fastq.gz

37613 B2_1_39_L001_R2_001.fastq.gz

132835 B2_20_74_L001_R1_001.fastq.gz

132835 B2_20_75_L001_R2_001.fastq.gz

45602 B2_2_40_L001_R1_001.fastq.gz

45602 B2_2_41_L001_R2_001.fastq.gz

59030 B2_3_42_L001_R1_001.fastq.gz

59030 B2_3_43_L001_R2_001.fastq.gz

11764 B2_4_44_L001_R1_001.fastq.gz

11764 B2_4_45_L001_R2_001.fastq.gz

78566 B2_5_46_L001_R1_001.fastq.gz

78566 B2_5_47_L001_R2_001.fastq.gz

136583 B2_6_48_L001_R1_001.fastq.gz

136583 B2_6_49_L001_R2_001.fastq.gz

72345 B2_7_50_L001_R1_001.fastq.gz

72345 B2_7_51_L001_R2_001.fastq.gz

61752 B2_8_52_L001_R1_001.fastq.gz

61752 B2_8_53_L001_R2_001.fastq.gz

86249 B2_9_54_L001_R1_001.fastq.gz

86249 B2_9_55_L001_R2_001.fastq.gz

35169 C1_10_174_L001_R1_001.fastq.gz

35169 C1_10_175_L001_R2_001.fastq.gz

26457 C1_11_176_L001_R1_001.fastq.gz

26457 C1_11_177_L001_R2_001.fastq.gz

2716 C1_12_178_L001_R1_001.fastq.gz

2716 C1_12_179_L001_R2_001.fastq.gz

1829 C1_13_180_L001_R1_001.fastq.gz

1829 C1_13_181_L001_R2_001.fastq.gz

37927 C1_14_182_L001_R1_001.fastq.gz

37927 C1_14_183_L001_R2_001.fastq.gz

46070 C1_15_184_L001_R1_001.fastq.gz

46070 C1_15_185_L001_R2_001.fastq.gz

37465 C1_16_186_L001_R1_001.fastq.gz

37465 C1_16_187_L001_R2_001.fastq.gz

44157 C1_18_188_L001_R2_001.fastq.gz

44157 C1_18_190_L001_R1_001.fastq.gz

57775 C1_19_189_L001_R2_001.fastq.gz

57775 C1_19_191_L001_R1_001.fastq.gz

23894 C1_1_156_L001_R1_001.fastq.gz

23894 C1_1_157_L001_R2_001.fastq.gz

350 C1_20_192_L001_R1_001.fastq.gz

350 C1_20_193_L001_R2_001.fastq.gz

79916 C1_2_158_L001_R1_001.fastq.gz

79916 C1_2_159_L001_R2_001.fastq.gz

32426 C1_3_160_L001_R1_001.fastq.gz

32426 C1_3_161_L001_R2_001.fastq.gz

16950 C1_4_162_L001_R1_001.fastq.gz

16950 C1_4_163_L001_R2_001.fastq.gz

77709 C1_5_164_L001_R1_001.fastq.gz

77709 C1_5_165_L001_R2_001.fastq.gz

60000 C1_6_166_L001_R1_001.fastq.gz

60000 C1_6_167_L001_R2_001.fastq.gz

37135 C1_7_168_L001_R1_001.fastq.gz

37135 C1_7_169_L001_R2_001.fastq.gz

135668 C1_8_170_L001_R1_001.fastq.gz

135668 C1_8_171_L001_R2_001.fastq.gz

38303 C1_9_172_L001_R1_001.fastq.gz

38303 C1_9_173_L001_R2_001.fastq.gz

277492 C2_11_212_L001_R1_001.fastq.gz

277492 C2_11_213_L001_R2_001.fastq.gz

2843 C2_12_214_L001_R1_001.fastq.gz

2843 C2_12_215_L001_R2_001.fastq.gz

22086 C2_13_216_L001_R1_001.fastq.gz

22086 C2_13_217_L001_R2_001.fastq.gz

15648 C2_14_218_L001_R1_001.fastq.gz

15648 C2_14_219_L001_R2_001.fastq.gz

15231 C2_15_220_L001_R2_001.fastq.gz

15231 C2_15_222_L001_R1_001.fastq.gz

5787 C2_16_221_L001_R2_001.fastq.gz

5787 C2_16_223_L001_R1_001.fastq.gz

4902 C2_17_224_L001_R1_001.fastq.gz

4902 C2_17_225_L001_R2_001.fastq.gz

674 C2_18_226_L001_R1_001.fastq.gz

674 C2_18_227_L001_R2_001.fastq.gz

1901 C2_19_228_L001_R1_001.fastq.gz

1901 C2_19_229_L001_R2_001.fastq.gz

137651 C2_1_194_L001_R1_001.fastq.gz

137651 C2_1_195_L001_R2_001.fastq.gz

8579 C2_20_230_L001_R1_001.fastq.gz

8579 C2_20_231_L001_R2_001.fastq.gz

148783 C2_2_196_L001_R1_001.fastq.gz

148783 C2_2_197_L001_R2_001.fastq.gz

109730 C2_3_198_L001_R1_001.fastq.gz

109730 C2_3_199_L001_R2_001.fastq.gz

339058 C2_4_200_L001_R1_001.fastq.gz

339058 C2_4_201_L001_R2_001.fastq.gz

316105 C2_5_202_L001_R1_001.fastq.gz

316105 C2_5_203_L001_R2_001.fastq.gz

181464 C2_6_204_L001_R1_001.fastq.gz

181464 C2_6_205_L001_R2_001.fastq.gz

115944 C2_7_206_L001_R1_001.fastq.gz

115944 C2_7_207_L001_R2_001.fastq.gz

173612 C2_8_208_L001_R1_001.fastq.gz

173612 C2_8_209_L001_R2_001.fastq.gz

112842 C2_9_210_L001_R1_001.fastq.gz

112842 C2_9_211_L001_R2_001.fastq.gz

9466 M1_11_238_L001_R2_001.fastq.gz

9466 M1_11_247_L001_R1_001.fastq.gz

719 M1_12_239_L001_R2_001.fastq.gz

719 M1_12_248_L001_R1_001.fastq.gz

110 M1_13_240_L001_R2_001.fastq.gz

110 M1_13_249_L001_R1_001.fastq.gz

335 M1_14_241_L001_R2_001.fastq.gz

335 M1_14_250_L001_R1_001.fastq.gz

32 M1_16_242_L001_R2_001.fastq.gz

32 M1_16_251_L001_R1_001.fastq.gz

37 M1_17_243_L001_R2_001.fastq.gz

37 M1_17_252_L001_R1_001.fastq.gz

12581 M1_18_244_L001_R2_001.fastq.gz

12581 M1_18_253_L001_R1_001.fastq.gz

9861 M1_19_245_L001_R2_001.fastq.gz

9861 M1_19_254_L001_R1_001.fastq.gz

70511 M1_1_232_L001_R1_001.fastq.gz

70511 M1_1_233_L001_R2_001.fastq.gz

1479 M1_20_246_L001_R2_001.fastq.gz

1479 M1_20_255_L001_R1_001.fastq.gz

85514 M1_3_234_L001_R1_001.fastq.gz

69875 M1_3_235_L001_R2_001.fastq.gz

181859 M1_4_236_L001_R1_001.fastq.gz

181859 M1_4_237_L001_R2_001.fastq.gz

118 M2_10_274_L001_R1_001.fastq.gz

118 M2_10_275_L001_R2_001.fastq.gz

108 M2_11_276_L001_R1_001.fastq.gz

108 M2_11_277_L001_R2_001.fastq.gz

123 M2_12_278_L001_R1_001.fastq.gz

123 M2_12_279_L001_R2_001.fastq.gz

2515 M2_13_280_L001_R1_001.fastq.gz

2515 M2_13_281_L001_R2_001.fastq.gz

921 M2_14_282_L001_R1_001.fastq.gz

921 M2_14_283_L001_R2_001.fastq.gz

2968 M2_15_284_L001_R1_001.fastq.gz

2968 M2_15_285_L001_R2_001.fastq.gz

671 M2_16_286_L001_R1_001.fastq.gz

671 M2_16_287_L001_R2_001.fastq.gz

664 M2_17_288_L001_R1_001.fastq.gz

664 M2_17_289_L001_R2_001.fastq.gz

2937 M2_18_290_L001_R1_001.fastq.gz

2937 M2_18_291_L001_R2_001.fastq.gz

162 M2_19_292_L001_R1_001.fastq.gz

162 M2_19_293_L001_R2_001.fastq.gz

702 M2_1_256_L001_R1_001.fastq.gz

702 M2_1_257_L001_R2_001.fastq.gz

207 M2_20_294_L001_R1_001.fastq.gz

207 M2_20_295_L001_R2_001.fastq.gz

259 M2_2_258_L001_R1_001.fastq.gz

259 M2_2_259_L001_R2_001.fastq.gz

174 M2_3_260_L001_R1_001.fastq.gz

174 M2_3_261_L001_R2_001.fastq.gz

738 M2_4_262_L001_R1_001.fastq.gz

738 M2_4_263_L001_R2_001.fastq.gz

53 M2_5_264_L001_R1_001.fastq.gz

53 M2_5_265_L001_R2_001.fastq.gz

308 M2_6_266_L001_R1_001.fastq.gz

308 M2_6_267_L001_R2_001.fastq.gz

717 M2_7_268_L001_R1_001.fastq.gz

717 M2_7_269_L001_R2_001.fastq.gz

16202 M2_8_270_L001_R1_001.fastq.gz

16202 M2_8_271_L001_R2_001.fastq.gz

232 M2_9_272_L001_R1_001.fastq.gz

232 M2_9_273_L001_R2_001.fastq.gz

123663 N1_10_94_L001_R1_001.fastq.gz

123663 N1_10_95_L001_R2_001.fastq.gz

90067 N1_11_96_L001_R1_001.fastq.gz

90067 N1_11_97_L001_R2_001.fastq.gz

89230 N1_12_98_L001_R1_001.fastq.gz

89230 N1_12_99_L001_R2_001.fastq.gz

20547 N1_13_100_L001_R1_001.fastq.gz

20547 N1_13_101_L001_R2_001.fastq.gz

63427 N1_14_102_L001_R1_001.fastq.gz

63427 N1_14_103_L001_R2_001.fastq.gz

20792 N1_15_106_L001_R2_001.fastq.gz

20792 N1_15_107_L001_R1_001.fastq.gz

826 N1_16_104_L001_R2_001.fastq.gz

826 N1_16_105_L001_R1_001.fastq.gz

325114 N1_17_108_L001_R1_001.fastq.gz

325114 N1_17_109_L001_R2_001.fastq.gz

96294 N1_18_110_L001_R1_001.fastq.gz

96294 N1_18_111_L001_R2_001.fastq.gz

157417 N1_19_112_L001_R1_001.fastq.gz

157417 N1_19_113_L001_R2_001.fastq.gz

4 N1_1_76_L001_R1_001.fastq.gz

4 N1_1_77_L001_R2_001.fastq.gz

134296 N1_20_114_L001_R1_001.fastq.gz

134296 N1_20_115_L001_R2_001.fastq.gz

1 N1_2_78_L001_R1_001.fastq.gz

1 N1_2_79_L001_R2_001.fastq.gz

273 N1_3_80_L001_R1_001.fastq.gz

273 N1_3_81_L001_R2_001.fastq.gz

866 N1_4_82_L001_R1_001.fastq.gz

866 N1_4_83_L001_R2_001.fastq.gz

12944 N1_5_84_L001_R1_001.fastq.gz

12944 N1_5_85_L001_R2_001.fastq.gz

16322 N1_6_86_L001_R1_001.fastq.gz

16322 N1_6_87_L001_R2_001.fastq.gz

12638 N1_7_88_L001_R1_001.fastq.gz

12638 N1_7_89_L001_R2_001.fastq.gz

40100 N1_8_90_L001_R1_001.fastq.gz

40100 N1_8_91_L001_R2_001.fastq.gz

127159 N1_9_92_L001_R1_001.fastq.gz

127159 N1_9_93_L001_R2_001.fastq.gz

124402 N2_10_134_L001_R1_001.fastq.gz

124402 N2_10_135_L001_R2_001.fastq.gz

8046 N2_11_136_L001_R1_001.fastq.gz

8046 N2_11_137_L001_R2_001.fastq.gz

103634 N2_12_138_L001_R1_001.fastq.gz

103634 N2_12_139_L001_R2_001.fastq.gz

122832 N2_13_140_L001_R1_001.fastq.gz

122832 N2_13_141_L001_R2_001.fastq.gz

137754 N2_14_142_L001_R1_001.fastq.gz

137754 N2_14_143_L001_R2_001.fastq.gz

124142 N2_15_144_L001_R1_001.fastq.gz

124142 N2_15_145_L001_R2_001.fastq.gz

168887 N2_16_146_L001_R1_001.fastq.gz

168887 N2_16_150_L001_R2_001.fastq.gz

215356 N2_17_147_L001_R1_001.fastq.gz

215356 N2_17_151_L001_R2_001.fastq.gz

32813 N2_18_148_L001_R1_001.fastq.gz

32813 N2_18_152_L001_R2_001.fastq.gz

15984 N2_19_149_L001_R1_001.fastq.gz

15984 N2_19_153_L001_R2_001.fastq.gz

53796 N2_1_116_L001_R1_001.fastq.gz

53796 N2_1_117_L001_R2_001.fastq.gz

89102 N2_20_154_L001_R1_001.fastq.gz

89102 N2_20_155_L001_R2_001.fastq.gz

63742 N2_2_118_L001_R1_001.fastq.gz

63742 N2_2_119_L001_R2_001.fastq.gz

3401 N2_3_120_L001_R1_001.fastq.gz

3401 N2_3_121_L001_R2_001.fastq.gz

1129 N2_4_122_L001_R2_001.fastq.gz

1129 N2_4_123_L001_R1_001.fastq.gz

78389 N2_5_124_L001_R1_001.fastq.gz

78389 N2_5_125_L001_R2_001.fastq.gz

28407 N2_6_126_L001_R1_001.fastq.gz

28407 N2_6_127_L001_R2_001.fastq.gz

139986 N2_7_128_L001_R1_001.fastq.gz

139986 N2_7_129_L001_R2_001.fastq.gz

94916 N2_8_130_L001_R1_001.fastq.gz

94916 N2_8_131_L001_R2_001.fastq.gz

177591 N2_9_132_L001_R1_001.fastq.gz

177591 N2_9_133_L001_R2_001.fastq.gz

It looks like M1_3 might be the culprit

1 Like
(Matthew Ryan Dillon) #15

Yep, I agree! Chat with your sequencing center - maybe the file wasn’t completely transferred when you procured it?

(Ariangela Davis) #17

Thank you for your help in figuring out the problem!

1 Like
(system) closed #18

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