Comments (3)
Hi Flora,
I think the traceback is probably telling a lot of the story here:
"/home/florathecat/anaconda3/lib/python3.6/gzip.py", line 482, in read', ' raise EOFError("Compressed file ended before the "', 'EOFError: Compressed file ended before the end-of-stream marker was reached']
Many file handling utilities, including programs like FastQC and bowtie will happily process gzipped files that don't have an EOF. As long as the truncation occurs at the end of a read (e.g. a multiple of 4), these tools won't even throw an error or warning. Python's file handler however doesn't like truncated gzipped files.
If you take a look at DRR015930 over in the SRA runbrowser, you'll see the files should be ~3GB combined while compressed and ~15GB when ucompressed. Since you've said that the files giving you errors are pretty small, <50mb, combined with the traceback I'm guessing these files didn't download correctly.
fastq-dump was giving me issues this morning trying to download DRR015930
off of SRA and I had to resort to going over to DDBJ to actually grab the data. I downloaded the bz2 compressed files, and converted them over to gzipped files.
$ du -sB MB DRR015930_1.fastq DRR015930_1.fastq.gz DRR015930_2.fastq DRR015930_2.fastq.gz
7596MB DRR015930_1.fastq
1738MB DRR015930_1.fastq.gz
7596MB DRR015930_2.fastq
1809MB DRR015930_2.fastq.gz
$ stringMLST.py --getMLST --species ecoli1 -P Ec
Database ready for escherichia coli#1
Ec
$ stringMLST.py --predict -P Ec/ecoli1 -1 DRR015930_1.fastq.gz -2 DRR015930_2.fastq.gz
Sample adk fumC gyrB icd mdh purA recA ST
DRR015930 2 79 59 2 2 2 2 260
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Hi Aroon,
Thanks! I didn't even realize that the files were corrupted. I downloaded the smaller files (ERR1777574) and indeed the files are bigger than the original ones that I had. The new files now gave me a ST. As to the large files (DRR015930) that gave me an empty result, fastq-dump gave me issues, too, so I am using DDBJ as you recommended.
Many Many Thanks and may you enjoy a great holiday season!
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Great! Have a great end of year as well :)
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