I got an error following error message on :
Failed to process Soy_CD.gz
java.util.zip.ZipException: Not in GZIP format
at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:166)
at java.base/java.util.zip.GZIPInputStream.(GZIPInputStream.java:80)
at java.base/java.util.zip.GZIPInputStream.(GZIPInputStream.java:92)
at uk.ac.babraham.FastQC.Utilities.MultiMemberGZIPInputStream.(MultiMemberGZIPInputStream.java:37)
at uk.ac.babraham.FastQC.Sequence.FastQFile.(FastQFile.java:80)
at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:87)
at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:152)
at uk.ac.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:121)
at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)
for this entry
|Sample Acess|Sample_ID|Url|
|SRR2048197|Soy_DA|https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR2048197/SRR2048197.1|
|SRR2048198|Soy_DB|https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR2048198/SRR2048198.1|
|SRR2048199|Soy_DC|https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR2048199/SRR2048199.1|
|SRR2048200|Soy_CD|https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR2048200/SRR2048200.1|
|SRR2048201|Soy_CE|https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR2048201/SRR2048201.1|
|SRR2048202|Soy_CF|https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR2048202/SRR2048202.1|
it seems that data type is not fastqsanger.gz but something else… I have changed the data type as fastq and this time I had the error below:
Failed to process Soy_DB
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn’t start with ‘@’
at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158)
at uk.ac.babraham.FastQC.Sequence.FastQFile.(FastQFile.java:89)
at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:87)
at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:152)
at uk.ac.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:121)
at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)
I tried to file type to be assigned automatically but it also did not work for me ?
How am I gonna know the file type for the SRA experiments of interest?