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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
GNU General Public License v2.0
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Can not read sequence #1 of 5 #220

Closed ghost closed 5 years ago

ghost commented 5 years ago

Dear tseemann

my sample.tab is

Isolate_1 /home/mars/Documents/Vibrios/19085D-01-01_S165_L007_R1_001.fastq.gz /home/mars/Documents/Vibrios/19085D-01-01_S165_L007_R2_001.fastq.gz Isolate_2 /home/mars/Documents/Vibrios/19085D-01-02_S166_L007_R1_001.fastq.gz /home/mars/Documents/Vibrios/19085D-01-02_S166_L007_R2_001.fastq.gz Isolate_3 /home/mars/Documents/Vibrios/19085D-01-03_S172_L007_R1_001.fastq.gz /home/mars/Documents/Vibrios/19085D-01-03_S172_L007_R2_001.fastq.gz Isolate_4 /home/mars/Documents/Vibrios/19085D-01-04_S167_L007_R1_001.fastq.gz /home/mars/Documents/Vibrios/19085D-01-04_S167_L007_R2_001.fastq.gz Isolate_5 /home/mars/Documents/Vibrios/19085D-01-05_S168_L007_R1_001.fastq.gz /home/mars/Documents/Vibrios/19085D-01-05_S168_L007_R2_001.fastq.gz Isolate_6 /home/mars/Documents/Vibrios/19085D-01-06_S169_L007_R1_001.fastq.gz /home/mars/Documents/Vibrios/19085D-01-06_S169_L007_R2_001.fastq.gz Isolate_7 /home/mars/Documents/Vibrios/19085D-01-07_S170_L007_R1_001.fastq.gz /home/mars/Documents/Vibrios/19085D-01-07_S170_L007_R2_001.fastq.gz Isolate_8 /home/mars/Documents/Vibrios/19085D-01-08_S171_L007_R1_001.fastq.gz /home/mars/Documents/Vibrios/19085D-01-08_S171_L007_R2_001.fastq.gz

As you can see, each lines are separated like you say in nullarbor page, but my prompt ansrwer is:

[10:02:07] Hello mars [10:02:07] This is nullarbor.pl 2.0.20181010 [10:02:07] Send complaints to Torsten Seemann [10:02:07] Scanning --ref for problematic sequence IDs... [10:02:07] Using reference genome: /home/mars/Documents/Vibrios/NC_004603.gbk [10:02:07] ERROR: Isolate 'Isolate_1' - can not read sequence #1 of 5 files: ''

Finally, my command line is:

nullarbor.pl --name Vp --mlst vparahaemolyticus --ref NC_004603.gbk --input samples.tab --outdir Vp_report

I installed all programs and database, everything is OK! And at this point, I don't know what I do.

Thank in advance!

tseemann commented 5 years ago

@mars3680 are the columns in samples.tab TAB separated?

Can you show me what cat -A samples.tab looks like?