cziegenhain
commented
5 years ago Hey,
Sorry that you are encountering issues!
It looks like none of the reads come out of the filtering step, hence the failures & instant mapping of 0 reads downstream. Could you check the content of the following output files : .BCstats.txt .filtered.tagged.unmapped.bam
This should tell us more about how the errors come about.
It could be that something is odd with the fastq files - although me and others have used data from GEO before but you never know with public data. (if you could send me a head of the fastq files too it would help to see if the read ID line contains something unexpected maybe!)
Regarding the read_layout: SE is correct as there is only one cDNA read so zUMIs detects that ;-)
Best, Christoph
PS: I changed the title of the issue so it's a bit more traceable.
cpchaney
Describe the bug Alignment is unsuccessful so that humphreys_human_snuc.filtered.tagged.Aligned.out.bam contains no sequences (samtools view humphreys_human_snuc.filtered.tagged.Aligned.out.bam | head -n 10 produces no output)
To Reproduce Provide the YAML file and full standard output. YAML: project: humphreys_human_snuc sequence_files: file1: name: /obfuscated/Documents/ncbi/public/fastq/SRR7648415_1.fastq.paired.fq.gz base_definition:
stdout: [W::bam_merge_core2] No @HD tag found. [E::sam_parse1] unrecognized type 7 [W::sam_read1] Parse error at line 198 [main_samview] truncated file. Error in (function (cl, name, valueClass) : assignment of an object of class “numeric” is not valid for @‘Dim’ in an object of class “dgTMatrix”; is(value, "integer") is not TRUE Calls: convert2countM -> .makewide -> ->
Execution halted
Warning message:
In fread(gtf, select = 1:2, header = F) :
Found and resolved improper quoting in first 100 rows. If the fields are not quoted (e.g. field separator does not appear within any field), try quote="" to avoid this warning.
Error in gzfile(file, "rb") : cannot open the connection
Calls: readRDS -> gzfile
In addition: Warning message:
In gzfile(file, "rb") :
cannot open compressed file '/obfuscated/Research/RBK/output/humphreys_human_snuc/zUMIs_output/expression/humphreys_human_snuc.dgecounts.rds', probable reason 'No such file or directory'
Execution halted
Screenshots If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
Additional context The dataset was generated by sequencing human single nuclei. The data are available from GEO under the accession GSE118184. The libraries were prepared for sequencing using the 10X Chromium system. The FASTQ files were downloaded from GEO with fastq-dump and preprocessed with fastq_pair to make sure that all reads have a mate.
The following additional observations might be informative.
Aug 05 07:51:42 ..... started STAR run Aug 05 07:51:45 ..... loading genome Aug 05 07:56:09 ..... processing annotations GTF Aug 05 07:56:39 ..... inserting junctions into the genome indices Aug 05 08:01:01 ..... started 1st pass mapping Aug 05 08:01:01 ..... finished 1st pass mapping Aug 05 08:01:02 ..... inserting junctions into the genome indices Aug 05 08:02:45 ..... started mapping Aug 05 08:02:46 ..... finished successfully