As reported in #57 , I encountered some trouble using mock 7 and 8.
I am using qiime 19.1
split_libraries_fastq.py -i mock7-forward-read.fastq -o split_libraries_M7 -m mock7_sample-metadata.tsv -b mock7-index-read.fastq.gz --rev_comp_mapping_barcodes
Traceback (most recent call last):
File "/usr/local/genome/VirtualEnv/qiime-1.9.1/bin/split_libraries_fastq.py", line 365, in
main()
File "/usr/local/genome/VirtualEnv/qiime-1.9.1/bin/split_libraries_fastq.py", line 344, in main
for fasta_header, sequence, quality, seq_id in seq_generator:
File "/usr/local/genome/VirtualEnv/qiime-1.9.1/lib/python2.7/site-packages/qiime/split_libraries_fastq.py", line 317, in process_fastq_single_end_read_file
parse_fastq(fastq_read_f, strict=False, phred_offset=phred_offset)):
File "/usr/local/genome/VirtualEnv/qiime-1.9.1/lib/python2.7/site-packages/skbio/parse/sequences/fastq.py", line 174, in parse_fastq
seqid)
skbio.parse.sequences._exception.FastqParseError: Failed qual conversion for seq id: ILLUMINA_0275:2:1101:1357:1952#ATAGGCGATCNN. This may be because you passed an incorrect value for phred_offset.
split_libraries_fastq.py -i mock8-forward-read.fastq.gz -o split_librariesM8 -m mock8_sample-metadata.tsv -b mock8-index-read.fastq.gz --rev_comp_mapping_barcodes --phred_offset 64
Traceback (most recent call last):
File "/usr/local/genome/VirtualEnv/qiime-1.9.1/bin/split_libraries_fastq.py", line 365, in
main()
File "/usr/local/genome/VirtualEnv/qiime-1.9.1/bin/split_libraries_fastq.py", line 344, in main
for fasta_header, sequence, quality, seq_id in seq_generator:
File "/usr/local/genome/VirtualEnv/qiime-1.9.1/lib/python2.7/site-packages/qiime/split_libraries_fastq.py", line 317, in process_fastq_single_end_read_file
parse_fastq(fastq_read_f, strict=False, phred_offset=phred_offset)):
File "/usr/local/genome/VirtualEnv/qiime-1.9.1/lib/python2.7/site-packages/skbio/parse/sequences/fastq.py", line 174, in parse_fastq
seqid)
skbio.parse.sequences._exception.FastqParseError: Failed qual conversion for seq id: ILLUMINA_0258:3:1101:1184:1974#NNNNNNNNNNNN. This may be because you passed an incorrect value for phred_offset.
It seems that the phred quality score is not valid.
The indicated sequence contain "i" quality character, so corresponding to ascii 105, which is out of the classical score scale.
I checked the sequence but the ascii value are between 66 and 104, so it should work.
Do you have same trouble ? What can I do to solve this ?
A final question, does the sequence still contains primer sequences ?