bcl2fastq No tiles were found to process
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Entering edit mode
7.1 years ago

Dear All,

I am quite a newbie for bcl2fastq software. I obtained my data from NextSeq500 system and trying to run bcl2fastq 2.0 for fastq conversion. But I am always getting error saying that "No tiles were found to process".

I have 6 same samples in all 4 lanes. I've checked all necessary files and were placed on right directories. I created my sample sheet by using IEM. I try to use different --tiles opt. parameters. Also --no-lane-splitting option with different configurations but nothing works. I read a lot however I haven't seen anyone had this error. So I am kind of afraid that this a basic problem. Could anyone help me to solve this?

Note: IEM doesn't create a "Lane" column that's why I write that one down. However I also tried with "Lane" as first column addition to samplsesheet below.

My SampleSheet:

[Header],,,,,,,,,

IEMFileVersion,4,,,,,,,,

Investigator Name,SK,,,,,,,,

Experiment Name,01.08.17-EXOME-RUN-1,,,,,,,,

Date,05.10.2017,,,,,,,,

Workflow,GenerateFASTQ,,,,,,,,

Application,NextSeq FASTQ Only,,,,,,,,

Assay,TruSight Enrichment,,,,,,,,

Description,,,,,,,,,

Chemistry,Amplicon,,,,,,,,

,,,,,,,,,

[Reads],,,,,,,,,

76,,,,,,,,,

76,,,,,,,,,

,,,,,,,,,

[Settings],,,,,,,,,

Adapter,CTGTCTCTTATACACATCT,,,,,,,,

,,,,,,,,,

[Data],,,,,,,,,

Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description

EXOM1,BARAN-CENGIZ,01.08.17-EXOME-RUN-1,A01,N701,TAAGGCGA,E502,ATAGAGAG,Deneme,Deneme

EXOM2,FERHAT-CEKMEZ,01.08.17-EXOME-RUN-1,A02,N702,CGTACTAG,E502,ATAGAGAG,Deneme,Deneme

EXOM3,MEHMET-AKIF,01.08.17-EXOME-RUN-1,A03,N703,AGGCAGAA,E502,ATAGAGAG,Deneme,Deneme

EXOM4,AYSE-ALINA,01.08.17-EXOME-RUN-1,A04,N704,TCCTGAGC,E502,ATAGAGAG,Deneme,Deneme

EXOM5,CEYHUN-YILMAZ-KAN,01.08.17-EXOME-RUN-1,A05,N705,GGACTCCT,E502,ATAGAGAG,Deneme,Deneme

EXOM6,CEYHUN-YILMAZ-DOKU,01.08.17-EXOME-RUN-1,A06,N707,CTCTCTAC,E502,ATAGAGAG,Deneme,Deneme

And error goes like this:

genus@acu-genus:/media/demo/170815_NB501568_0002_AH257CBGX3$ /usr/local/bin/bcl2fastq --runfolder-dir /media/demo/170815_NB501568_0002_AH257CBGX3 --output-dir /media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/BaseCalls

BCL to FASTQ file converter

bcl2fastq v2.20.0.422

Copyright (c) 2007-2017 Illumina, Inc.

2017-10-14 07:38:54 [1816880] Command-line invocation: /usr/local/bin/bcl2fastq --runfolder-dir /media/demo/170815_NB501568_0002_AH257CBGX3 --output-dir /media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/BaseCalls

2017-10-14 07:38:54 [1816880] INFO: Minimum log level: INFO

2017-10-14 07:38:54 [1816880] INFO: Sample sheet: '/media/demo/170815_NB501568_0002_AH257CBGX3/SampleSheet.csv'

2017-10-14 07:38:54 [1816880] INFO: Runfolder path: '/media/demo/170815_NB501568_0002_AH257CBGX3'

2017-10-14 07:38:54 [1816880] INFO: Input path: '/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/BaseCalls/'

2017-10-14 07:38:54 [1816880] INFO: Intensities path: '/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/'

2017-10-14 07:38:54 [1816880] INFO: Output path: '/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/BaseCalls'

2017-10-14 07:38:54 [1816880] INFO: InterOp path: '/media/demo/170815_NB501568_0002_AH257CBGX3/InterOp/'

2017-10-14 07:38:54 [1816880] INFO: Stats path: '/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/BaseCalls/Stats/'

2017-10-14 07:38:54 [1816880] INFO: Reports path: '/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities/BaseCalls/Reports/'

2017-10-14 07:38:54 [1816880] INFO: Detected CPUs: 16

2017-10-14 07:38:54 [1816880] INFO: Loading threads: 4

2017-10-14 07:38:54 [1816880] INFO: Processing threads: 16

2017-10-14 07:38:54 [1816880] INFO: Writing threads: 4

2017-10-14 07:38:54 [1816880] INFO: Allowed barcode mismatches: 1

2017-10-14 07:38:54 [1816880] INFO: Tiles: <all>

2017-10-14 07:38:54 [1816880] INFO: Minimum trimmed read length: 35

2017-10-14 07:38:54 [1816880] INFO: Use bases masks: <none>

2017-10-14 07:38:54 [1816880] INFO: Mask short adapter reads: 22

2017-10-14 07:38:54 [1816880] INFO: Adapter stringency: 0.9

2017-10-14 07:38:54 [1816880] INFO: Adapter trimming method: Allow matches with indels

2017-10-14 07:38:54 [1816880] INFO: Ignore missing BCLs: NO

2017-10-14 07:38:54 [1816880] INFO: Ignore missing filters: NO

2017-10-14 07:38:54 [1816880] INFO: Ignore missing positions: NO

2017-10-14 07:38:54 [1816880] INFO: Ignore missing controls: NO

2017-10-14 07:38:54 [1816880] INFO: Include non-PF clusters: NO

2017-10-14 07:38:54 [1816880] INFO: Create FASTQs for index reads: NO

2017-10-14 07:38:54 [1816880] INFO: Use bgzf compression for FASTQ files: YES

2017-10-14 07:38:54 [1816880] INFO: FASTQ compression level: 4

2017-10-14 07:38:54 [1816880] INFO: RunInfo.xml: '"/media/demo/170815_NB501568_0002_AH257CBGX3/RunInfo.xml"'

2017-10-14 07:38:54 [1816880] INFO: Lane: 1

2017-10-14 07:38:54 [1816880] INFO: Mask:

2017-10-14 07:38:54 [1816880] INFO: Sample: #0 'unknown' 'Undetermined' [default]

2017-10-14 07:38:54 [1816880] INFO: Sample: #1 'EXOM1' 'BARAN-CENGIZ' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TAAGGCGA+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #2 'EXOM2' 'FERHAT-CEKMEZ' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CGTACTAG+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #3 'EXOM3' 'MEHMET-AKIF' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'AGGCAGAA+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #4 'EXOM4' 'AYSE-ALINA' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TCCTGAGC+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #5 'EXOM5' 'CEYHUN-YILMAZ-KAN' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'GGACTCCT+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #6 'EXOM6' 'CEYHUN-YILMAZ-DOKU' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CTCTCTAC+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Read: 1 data read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76

2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

2017-10-14 07:38:54 [1816880] INFO: Read: 1 index read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 77,78,79,80,81,82,83,84

2017-10-14 07:38:54 [1816880] INFO: Read: 2 index read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 85,86,87,88,89,90,91,92

2017-10-14 07:38:54 [1816880] INFO: Read: 2 data read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167, 168

2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

2017-10-14 07:38:54 [1816880] INFO: Lane: 2

2017-10-14 07:38:54 [1816880] INFO: Mask:

2017-10-14 07:38:54 [1816880] INFO: Sample: #0 'unknown' 'Undetermined' [default]

2017-10-14 07:38:54 [1816880] INFO: Sample: #1 'EXOM1' 'BARAN-CENGIZ' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TAAGGCGA+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #2 'EXOM2' 'FERHAT-CEKMEZ' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CGTACTAG+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #3 'EXOM3' 'MEHMET-AKIF' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'AGGCAGAA+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #4 'EXOM4' 'AYSE-ALINA' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TCCTGAGC+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #5 'EXOM5' 'CEYHUN-YILMAZ-KAN' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'GGACTCCT+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #6 'EXOM6' 'CEYHUN-YILMAZ-DOKU' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CTCTCTAC+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Read: 1 data read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76

2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

2017-10-14 07:38:54 [1816880] INFO: Read: 1 index read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 77,78,79,80,81,82,83,84

2017-10-14 07:38:54 [1816880] INFO: Read: 2 index read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 85,86,87,88,89,90,91,92

2017-10-14 07:38:54 [1816880] INFO: Read: 2 data read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168

2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

2017-10-14 07:38:54 [1816880] INFO: Lane: 3

2017-10-14 07:38:54 [1816880] INFO: Mask:

2017-10-14 07:38:54 [1816880] INFO: Sample: #0 'unknown' 'Undetermined' [default]

2017-10-14 07:38:54 [1816880] INFO: Sample: #1 'EXOM1' 'BARAN-CENGIZ' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TAAGGCGA+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #2 'EXOM2' 'FERHAT-CEKMEZ' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CGTACTAG+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #3 'EXOM3' 'MEHMET-AKIF' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'AGGCAGAA+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #4 'EXOM4' 'AYSE-ALINA' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TCCTGAGC+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #5 'EXOM5' 'CEYHUN-YILMAZ-KAN' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'GGACTCCT+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #6 'EXOM6' 'CEYHUN-YILMAZ-DOKU' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CTCTCTAC+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Read: 1 data read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76

2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

2017-10-14 07:38:54 [1816880] INFO: Read: 1 index read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 77,78,79,80,81,82,83,84

2017-10-14 07:38:54 [1816880] INFO: Read: 2 index read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 85,86,87,88,89,90,91,92

2017-10-14 07:38:54 [1816880] INFO: Read: 2 data read

2017-10-14 07:38:54 [1816880] INFO: Cycles:

93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168

2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

2017-10-14 07:38:54 [1816880] INFO: Lane: 4

2017-10-14 07:38:54 [1816880] INFO: Mask:

2017-10-14 07:38:54 [1816880] INFO: Sample: #0 'unknown' 'Undetermined' [default]

2017-10-14 07:38:54 [1816880] INFO: Sample: #1 'EXOM1' 'BARAN-CENGIZ' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TAAGGCGA+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #2 'EXOM2' 'FERHAT-CEKMEZ' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CGTACTAG+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #3 'EXOM3' 'MEHMET-AKIF' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'AGGCAGAA+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #4 'EXOM4' 'AYSE-ALINA' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'TCCTGAGC+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #5 'EXOM5' 'CEYHUN-YILMAZ-KAN' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'GGACTCCT+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Sample: #6 'EXOM6' 'CEYHUN-YILMAZ-DOKU' [Deneme]

2017-10-14 07:38:54 [1816880] INFO: Barcode: 'CTCTCTAC+ATAGAGAG'

2017-10-14 07:38:54 [1816880] INFO: Read: 1 data read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76

2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

2017-10-14 07:38:54 [1816880] INFO: Read: 1 index read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 77,78,79,80,81,82,83,84

2017-10-14 07:38:54 [1816880] INFO: Read: 2 index read

2017-10-14 07:38:54 [1816880] INFO: Cycles: 85,86,87,88,89,90,91,92

2017-10-14 07:38:54 [1816880] INFO: Read: 2 data read

2017-10-14 07:38:54 [1816880] INFO: Cycles:

93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168

2017-10-14 07:38:54 [1816880] INFO: Adapter: CTGTCTCTTATACACATCT (trim adapter)

2017-10-14 07:38:54 [1816880] ERROR: bcl2fastq::common::Exception: 2017-Oct-14 07:38:54: Success (0): /TeamCityBuildAgent/work/556afd631a5b66d8/src/cxx/lib/layout/Layout.cpp(1194): Throw in function static void bcl2fastq::layout::TileLayoutDetector::detectTileLayout(const std::vector<std::basic_string<char> >&, const bcl2fastq::layout::RunInfoXml&, const bcl2fastq::config::SampleSheetCsv&, const boost::filesystem::path&, std::vector<bcl2fastq::layout::laneinfo>&, bcl2fastq::common::TileFileMap&, bcl2fastq::common::NumBasesPerByte&, bcl2fastq::common::TileAggregationMode, bool, bcl2fastq::common::CycleNumber, bcl2fastq::common::CycleNumber, bool) Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::inputdataerror> std::exception::what: No tiles were found to process.
next-gen sequence software error • 5.2k views
ADD COMMENT •
1
Entering edit mode

seems that your loc files of bcl files are not found. Can you show what you have under dir "Data/Intensities"?

$ tree L*
L001
└── s_1.locs
L002
└── s_2.locs
L003
└── s_3.locs
L004
└── s_4.locs

and

$ tree BaseCalls/L001 | head
BaseCalls/L001
├── 0001.bcl.bgzf
├── 0001.bcl.bgzf.bci
├── 0002.bcl.bgzf
├── 0002.bcl.bgzf.bci
├── 0003.bcl.bgzf
├── 0003.bcl.bgzf.bci
├── 0004.bcl.bgzf
├── 0004.bcl.bgzf.bci
├── 0005.bcl.bgzf
$ tree BaseCalls/L001 | tail
├── 0166.bcl.bgzf
├── 0166.bcl.bgzf.bci
├── 0167.bcl.bgzf
├── 0167.bcl.bgzf.bci
├── 0168.bcl.bgzf
├── 0168.bcl.bgzf.bci
├── s_1.bci
└── s_1.filter
ADD REPLY •
0
Entering edit mode

Thank you for reply. You can see the directories...

genus@acu-genus:/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities$ tree | head

└── BaseCalls
    └── L001
        ├── 0001.bcl.bgzf
        ├── 0001.bcl.bgzf.bci
        ├── 0002.bcl.bgzf
        ├── 0002.bcl.bgzf.bci
        ├── 0003.bcl.bgzf
        ├── 0003.bcl.bgzf.bci
        ├── 0004.bcl.bgzf

genus@acu-genus:/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities$ tree | tail
        ├── 0096.bcl.bgzf.bci
        ├── 0097.bcl.bgzf
        ├── 0097.bcl.bgzf.bci
        ├── 0098.bcl.bgzf
        ├── 0098.bcl.bgzf.bci
        ├── 0099.bcl.bgzf
        ├── 0099.bcl.bgzf.bci
        └── 0100.bcl.bgzf

2 directories, 197 files

And

genus@acu-genus:/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities$ tree BaseCalls/L001 | head
BaseCalls/L001
├── 0001.bcl.bgzf
├── 0001.bcl.bgzf.bci
├── 0002.bcl.bgzf
├── 0002.bcl.bgzf.bci
├── 0003.bcl.bgzf
├── 0003.bcl.bgzf.bci
├── 0004.bcl.bgzf
├── 0004.bcl.bgzf.bci
├── 0005.bcl.bgzf

genus@acu-genus:/media/demo/170815_NB501568_0002_AH257CBGX3/Data/Intensities$ tree BaseCalls/L001 | tail
├── 0096.bcl.bgzf.bci
├── 0097.bcl.bgzf
├── 0097.bcl.bgzf.bci
├── 0098.bcl.bgzf
├── 0098.bcl.bgzf.bci
├── 0099.bcl.bgzf
├── 0099.bcl.bgzf.bci
└── 0100.bcl.bgzf

0 directories, 197 files
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0
Entering edit mode
7.1 years ago

The image link from my terminal showing directories. Better that way:/

http://uploads.im/y0K8r.jpg

So there are missing folders at intensities directory?
ADD COMMENT •
0
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you don't have the locs files nor the .filter in the BaseCalls.

Did you copy the folder from the sequencer to other place just when the run finished? Take into account that when the NextSeq says it has finished the run (it is free for another run), it still spent one hour or so post-processing things in the finished run. I don't know exactly when this process ends but as a thumb rule, before copy the data, I look at the timestamp of the folder and I don't copy anything until the modification time in the folder is not at least 40 minutes ago.

Could this be your problem?

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