diff --git a/README.md b/README.md index fd70fc6..77af2a9 100644 --- a/README.md +++ b/README.md @@ -63,9 +63,10 @@ The sample ERRxxxxx contains a single strain belonging to lineage 2. This typing ### Error handling
When fastlin cannot read a fastq file (e.g. faulty record within the fastq file, corrupt gzip file), it stops scanning it, re-initialise all values to 0 and report the error message in the last field of the output file. Here is an example of output with 3 different errors:
-> #sample nb_files k_cov mixture lineages log_barcodes log_errors -dummy1 single 0 no Error in file "reads/dummy1.fastq.gz": FASTQ parse error: sequence length is 150, but quality length is 50 (record 'ERR551806.5' at line 17). -dummy2 single 0 no Error in file "reads/dummy2.fastq.gz": invalid gzip header + +> #sample nb_files k_cov mixture lineages log_barcodes log_errors +dummy1 single 0 no Error in file "reads/dummy1.fastq.gz": FASTQ parse error: sequence length is 150, but quality length is 50 (record 'ERR551806.5' at line 17). +dummy2 single 0 no Error in file "reads/dummy2.fastq.gz": invalid gzip header dummy3 single 0 no Error in file "reads/dummy3.fastq.gz": corrupt deflate stream ### TO DO LIST