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Old 04-02-2019, 04:48 PM   #1
jmlabioinfo
Junior Member
 
Location: USA

Join Date: Apr 2019
Posts: 1
Unhappy Tile is missing

Hi all,

I received some fastq files from a PE HiSeq and when I tried to isolate N reads using the "fastq_illumina_reads -N" I got the following error:

Input error: file 'STDIN' line 1: Expecting Illumina-CASAVA1.8 ID line structure (@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos> <read>:<is filtered>:<control number>:<index sequence>) - got '@HS34_23148:4:1313:16347:42480/1' (Can't extract 'Tile’)



The header of the file shows:
@HS34_23148:4:2106:12625:73859/2
CACCAGCTGAGAGAGATGCTCGCCGTTGACTGACGAACTGAATTCCCAGTTCACGGCGGTATGGAATACCGTCGT
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@HS34_23148:4:1114:12855:77248/2
CTCGCCGTTGACTGACGAACTGAATTCCCAGTTCACGGCGGTATGGAATACCGTCGTCGCAGAGCTCAACGGTGA
+
BBBBBFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFF
@HS34_23148:4:1311:2663:94744/2
CTCGACAGATATTGATTGTCGTCACCGTTGAGCTCTGCGACGACGGTATTCCATACCGCCGTGAACTGGGAATTC

Does anyone already get the same problem with the tile coordinates?
(I could ask the facility who sent me the files an explanation but I'm not sure if the problem come from me or not)

Thank you
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Old 04-03-2019, 02:12 PM   #2
kmcarr
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Location: USA, Midwest

Join Date: May 2008
Posts: 1,172
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Quote:
Originally Posted by jmlabioinfo View Post
Hi all,

I received some fastq files from a PE HiSeq and when I tried to isolate N reads using the "fastq_illumina_reads -N" I got the following error:

Input error: file 'STDIN' line 1: Expecting Illumina-CASAVA1.8 ID line structure (@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos> <read>:<is filtered>:<control number>:<index sequence>) - got '@HS34_23148:4:1313:16347:42480/1' (Can't extract 'Tile’)



The header of the file shows:
@HS34_23148:4:2106:12625:73859/2
CACCAGCTGAGAGAGATGCTCGCCGTTGACTGACGAACTGAATTCCCAGTTCACGGCGGTATGGAATACCGTCGT
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@HS34_23148:4:1114:12855:77248/2
CTCGCCGTTGACTGACGAACTGAATTCCCAGTTCACGGCGGTATGGAATACCGTCGTCGCAGAGCTCAACGGTGA
+
BBBBBFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFF
@HS34_23148:4:1311:2663:94744/2
CTCGACAGATATTGATTGTCGTCACCGTTGAGCTCTGCGACGACGGTATTCCATACCGCCGTGAACTGGGAATTC

Does anyone already get the same problem with the tile coordinates?
(I could ask the facility who sent me the files an explanation but I'm not sure if the problem come from me or not)

Thank you
It looks like you got hold of a very old (in Illumina time scale) FastQ file. Have a look at the Illumina sequence identifiers discussion on the FastQ format Wikipedia page. The sequence headers in your file are the pre-CASAVA 1.8 format. The software you are trying to use (fastq_illumina_reads) is expecting the header format to be the post-CASAVA 1.8 format. I can't remember when that format version was first introduced but it was years ago.

What software package is the fastq_illumina_reads program from? Does it have a command line option to switch between the old and new FastQ sequence ID line formats?
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Old 08-04-2019, 01:00 PM   #3
JerryEckel
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Location: London, UK

Join Date: Aug 2019
Posts: 3
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Quote:
Originally Posted by kmcarr View Post
It looks like you got hold of a very old (in Illumina time scale) FastQ file. Have a look at the https://www.weareteacherfinder.com/b...dent-problems/ discussion on the FastQ format Wikipedia page. The sequence headers in your file are the pre-CASAVA 1.8 format. The software you are trying to use (fastq_illumina_reads) is expecting the header format to be the post-CASAVA 1.8 format. I can't remember when that format version was first introduced but it was years ago.

What software package is the fastq_illumina_reads program from? Does it have a command line option to switch between the old and new FastQ sequence ID line formats?
Thanks for the info. I tried different ways, but they didn't work. That is the reason I started to look for the new information. And found this.
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