STAR 2.5.3 Empty SAM/BAM output (Number of input reads | 0)

[Mazdak Salavati]

I have been trying to use STAR for mapping bovine (Cow) RNA-Seq data (SR 75nt) on UMD3.1.1 assembly. As the libraries were sequenced in two runs, I had to cat the fastq files as following: 

#!/bin/bash

mkdir -p ./Merged;

for f in "./"*_2016*.fastq.gz;

do

find ./ -iname "*${f:14:16}*" |xargs cat > ./Merged/${f:14:16}.fastq.gz

echo "Merger is done for ${f:14:16}" 

done;

The output fastq.gz file passes the FastQC with no errors at all and I couldn't find any other error in checksum or header/EOF section. 

Once I try to map/align it with STAR (1pass only and 2pass mode both) : 

~/Progz/STAR/bin/Linux_x86_64/STAR 

--runThreadN 8 

--runMode alignReads 

--genomeDir ../ref/STAR_ref/ 

--readFilesCommand zcat 

--readFilesIn ../GplusE_Data/Merged/Blood010001_lib1.fastq.gz 

--outFileNamePrefix ../Output/STAR_bams/Blood010001_lib1 

--runDirPerm User_RWX 

--outSAMtype BAM SortedByCoordinate 

--outSAMstrandField intronMotif 

--bamRemoveDuplicatesType UniqueIdenticalNotMulti 

--quantMode GeneCounts 

--twopassMode None 

I get an empty BAM file output as STAR doesn't read in the file. The final.out file looks as following: 

Started job on | Mar 28 13:53:00

Started mapping on | Mar 28 13:59:35

Finished on | Mar 28 13:59:38

Mapping speed, Million of reads per hour | 0.00

                          Number of input reads | 0

                      Average input read length | 0

                                    UNIQUE READS:

                   Uniquely mapped reads number | 0

                        Uniquely mapped reads % | 0.00%

                          Average mapped length | 0.00

                       Number of splices: Total | 0

            Number of splices: Annotated (sjdb) | 0

                       Number of splices: GT/AG | 0

                       Number of splices: GC/AG | 0

                       Number of splices: AT/AC | 0

               Number of splices: Non-canonical | 0

                      Mismatch rate per base, % | -nan%

                         Deletion rate per base | 0.00%

                        Deletion average length | 0.00

                        Insertion rate per base | 0.00%

                       Insertion average length | 0.00

                             MULTI-MAPPING READS:

        Number of reads mapped to multiple loci | 0

             % of reads mapped to multiple loci | 0.00%

        Number of reads mapped to too many loci | 0

             % of reads mapped to too many loci | 0.00%

                                  UNMAPPED READS:

       % of reads unmapped: too many mismatches | 0.00%

                 % of reads unmapped: too short | 0.00%

                     % of reads unmapped: other | 0.00%

                                  CHIMERIC READS:

                       Number of chimeric reads | 0

                            % of chimeric reads | 0.00%

I would appreciate any suggestions and helpful tips. 

Thanks.

[Alexander Dobin]

Hi  Mazdak,

please try to run STAR on an uncompressed file without  --readFilesCommand zcat .

If it works, it may indicate that there is a problem with fifo files on your partition. To check that, inside the STAR run directory, please try

$ mkfifo test1

Cheers

Alex

[Jack Yen]

What's the alternative if the system is not compatible with fifo files? Is unzipped fastq the only way to do it? Thanks 

[Alexander Dobin]

https://groups.google.com/d/msg/rna-star/MQdL1WxkAAw/eG6EatoOCgAJ