STAR only takes the first paired fastq files when there are multiple paired fastq file input

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What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?

I have multiple gzipped fastq file:

I run STAR with --readFilesIn set to be: 

--readFilesIn 
CRC0321-1_FCC4JJ9ACXX_L6_HUMhiaTACYRBAPEI-220_1.fq.gz,CRC0321-1_FCC4JJ9ACXX_L7_H
UMhiaTACYRBAPEI-220_1.fq.gz,CRC0321-1_FCC4JJ9ACXX_L8_HUMhiaTACYRBAPEI-220_1.fq.g
z 
CRC0321-1_FCC4JJ9ACXX_L6_HUMhiaTACYRBAPEI-220_2.fq.gz,CRC0321-1_FCC4JJ9ACXX_L7_H
UMhiaTACYRBAPEI-220_2.fq.gz,CRC0321-1_FCC4JJ9ACXX_L8_HUMhiaTACYRBAPEI-220_2.fq.g
z

Below is the ending part of the log generated by STAR
...
Starting to map file # 0
mate 1:   
/home/hbi16088/data/projects/pdx/fastq/CRC0321-1_FCC4JJ9ACXX_L6_HUMhiaTACYRBAPEI
-220_1.fq.gz
mate 2:   
/home/hbi16088/data/projects/pdx/fastq/CRC0321-1_FCC4JJ9ACXX_L6_HUMhiaTACYRBAPEI
-220_2.fq.gz
Created thread # 7
Created thread # 8
Created thread # 9
Completed: thread #7
Completed: thread #1
Completed: thread #5
Completed: thread #3
Completed: thread #2
Completed: thread #4
Completed: thread #6
Completed: thread #9
Completed: thread #0
Joined thread # 1
Joined thread # 2
Joined thread # 3
Joined thread # 4
Joined thread # 5
Joined thread # 6
Joined thread # 7
Completed: thread #8
Joined thread # 8
Joined thread # 9
ALL DONE!
--genomeLoad=LoadAndKeep .

STAR only used the first pair of fastq file instead of all three paired fastq 
files.

What version of the product are you using? On what operating system?

STAR svn revision compiled=STAR_2.3.1z4_r419

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 3 Jun 2014 at 2:51

[GoogleCodeExporter]

Hi,

I have exactly the same issue. Did you find a solution ?

Thanks

Original comment by [email protected] on 22 Oct 2014 at 4:19

[GoogleCodeExporter]

Bump. Any solution to this? I just discovered the same issue, after about a 
full week of aligning! Thanks, Craig

Original comment by [email protected] on 28 Oct 2014 at 5:15

[GoogleCodeExporter]

Hi Craig,

I used star 2.4.0a instead of star 2.4.0d I was using before. It seems that 
star 2.4.0d has some issues with multiple files.

See https://groups.google.com/forum/#!topic/rna-star/xBeqwANqGc8

Best,
Fanny

Original comment by [email protected] on 28 Oct 2014 at 6:07

[GoogleCodeExporter]

There is a fix in star STAR_2.4.0e for this. See:  
https://groups.google.com/forum/#!msg/rna-star/xBeqwANqGc8/ECnOc2S7zdUJ

Original comment by [email protected] on 28 Oct 2014 at 6:39