Question: Hisat error: 'NoneType' object has no attribute 'file_name'
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6 months ago by
chenzhuod30 wrote:


I create a workflow using local galaxy. PE RNA-Seq data after trimming are mapped against genome by Hisat. The input file is a collection including two PE RNA-Seq. When I run this process in workflow, one of them is error (But actually, it have been done successfully, and I can find the output file in galaxy file folder).

The error is : Could not display BAM file, error was: 'NoneType' object has no attribute 'file_name'.

And Fatal error: Exit code 134 () Settings: Output files: "genome..ht2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Local offset rate: 3 (one in 8) Local fTable chars: 6 Local sequence length: 57344 Local sequence overlap between two consecutive indexes: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void:8, int:4, long:8, size_t:8 Input files DNA, FASTA: genome.fa Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 Time to read SNPs and splice sites: 00:00:00 Using parameters --bmax 1028635 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 1028635 --dcv 1024 Constructing suffix-array element generator Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering GFM loop Exited GFM loop fchr[A]: 0 fchr[C]: 1402333 fchr[G]: 2741132 fchr[T]: 4094156 fchr[$]: 5486054 Exiting GFM::buildToDisk() Returning from initFromVector Wrote 6356107 bytes to primary GFM file: genome.1.ht2 Wrote 1371520 bytes to secondary GFM file: genome.2.ht2 Re-opening _in1 and _in2 as input streams Returning from GFM constructor Returning from initFromVector Wrote 103525261 bytes to primary GFM file: genome.5.ht2 Wrote 1385286 bytes to secondary GFM file: genome.6.ht2 Re-opening _in5 and _in5 as input streams Returning from HierEbwt constructor Headers: len: 5486054 gbwtLen: 5486055 nodes: 5486055 sz: 1371514 gbwtSz: 1371514 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 0 eftabSz: 0 ftabLen: 1048577 ftabSz: 4194308 offsLen: 342879 offsSz: 1371516 lineSz: 64 sideSz: 64 sideGbwtSz: 48 sideGbwtLen: 192 numSides: 28574 numLines: 28574 gbwtTotLen: 1828736 gbwtTotSz: 1828736 reverse: 0 linearFM: Yes Total time for call to driver() for forward index: 00:00:04 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): hisat2-align exited with value 134

What's the matter?

rna-seq • 255 views
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