Bowtie2 exception with rsem

[onthefly]

Hello

I am using rsem-calculate-expression (with bowtie2) for mapping fastq files (input) to the reference (prepared using rsem-prepare-reference).
The total number of samples is 6.
The mapping went fine with the first two samples, but the command got interrupted becuase I accidently switched off my system
Anyway after resuming the command, I am not able to map any of my remaining 4 samples. For each case the output is:

bowtie2 -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 8 -k 200 -x /media/RSEM_Map/reference/ref -1 /media/Fastq/Sample3_R1_001_1.fastq,/media/Fastq/Sample3_R1_002_1.fastq,/media/Fastq/Sample3_R1_003_1.fastq,/media/Fastq/Sample3_R1_004_1.fastq,/media/Fastq/Sample3_R1_005_1.fastq,/media/Fastq/Sample3_R1_006_1.fastq,/media/Fastq/Sample3_R1_007_1.fastq,/media/Fastq/Sample3_R1_008_1.fastq,/media/Fastq/Sample3_R1_009_1.fastq,/media/Fastq/Sample3_R1_010_1.fastq,/media/Fastq/Sample3_R1_011_1.fastq,/media/Fastq/Sample3_R1_012_1.fastq,/media/Fastq/Sample3_R1_013_1.fastq,/media/Fastq/Sample3_R1_014_1.fastq -2 /media/Fastq/Sample3_R2_001_2.fastq,/media/Fastq/Sample3_R2_002_2.fastq,/media/Fastq/Sample3_R2_003_2.fastq,/media/Fastq/Sample3_R2_004_2.fastq,/media/Fastq/Sample3_R2_005_2.fastq,/media/Fastq/Sample3_R2_006_2.fastq,/media/Fastq/Sample3_R2_007_2.fastq,/media/Fastq/Sample3_R2_008_2.fastq,/media/Fastq/Sample3_R2_009_2.fastq,/media/Fastq/Sample3_R2_010_2.fastq,/media/Fastq/Sample3_R2_011_2.fastq,/media/Fastq/Sample3_R2_012_2.fastq,/media/Fastq/Sample3_R2_013_2.fastq,/media/Fastq/Sample3_R2_014_2.fastq | /home//Biotools/sam/samtools view -S -b -o /media/RSEM_Map/Sample3_quals.temp/Sample3_quals.bam -
Error reading RefRecord 'first' flag
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home//Biotools/bowtie2-align --wrapper basic-0 -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 8 -k 200 -x /media/RSEM_Map/reference/ref -1 /media/Fastq/Sample3_R1_001_1.fastq,/media/Fastq/Sample3_R1_002_1.fastq,/media/Fastq/Sample3_R1_003_1.fastq,/media/Fastq/Sample3_R1_004_1.fastq,/media/Fastq/Sample3_R1_005_1.fastq,/media/Fastq/Sample3_R1_006_1.fastq,/media/Fastq/Sample3_R1_007_1.fastq,/media/Fastq/Sample3_R1_008_1.fastq,/media/Fastq/Sample3_R1_009_1.fastq,/media/Fastq/Sample3_R1_010_1.fastq,/media/Fastq/Sample3_R1_011_1.fastq,/media/Fastq/Sample3_R1_012_1.fastq,/media/Fastq/Sample3_R1_013_1.fastq,/media/Fastq/Sample3_R1_014_1.fastq -2 /media/Fastq/Sample3_R2_001_2.fastq,/media/Fastq/Sample3_R2_002_2.fastq,/media/Fastq/Sample3_R2_003_2.fastq,/media/Fastq/Sample3_R2_004_2.fastq,/media/Fastq/Sample3_R2_005_2.fastq,/media/Fastq/Sample3_R2_006_2.fastq,/media/Fastq/Sample3_R2_007_2.fastq,/media/Fastq/Sample3_R2_008_2.fastq,/media/Fastq/Sample3_R2_009_2.fastq,/media/Fastq/Sample3_R2_010_2.fastq,/media/Fastq/Sample3_R2_011_2.fastq,/media/Fastq/Sample3_R2_012_2.fastq,/media/Fastq/Sample3_R2_013_2.fastq,/media/Fastq/Sample3_R2_014_2.fastq 
bowtie2-align exited with value 1
[samopen] SAM header is present: 31426 sequences.
[sam_read1] reference 'ID:bowtie2	PN:bowtie2	VN:2.1.0
' is recognized as '*'.
[main_samview] truncated file.
"bowtie2 -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 8 -k 200 -x /media/RSEM_Map/reference/ref -1 /media/Fastq/Sample3_R1_001_1.fastq,/media/Fastq/Sample3_R1_002_1.fastq,/media/Fastq/Sample3_R1_003_1.fastq,/media/Fastq/Sample3_R1_004_1.fastq,/media/Fastq/Sample3_R1_005_1.fastq,/media/Fastq/Sample3_R1_006_1.fastq,/media/Fastq/Sample3_R1_007_1.fastq,/media/Fastq/Sample3_R1_008_1.fastq,/media/Fastq/Sample3_R1_009_1.fastq,/media/Fastq/Sample3_R1_010_1.fastq,/media/Fastq/Sample3_R1_011_1.fastq,/media/Fastq/Sample3_R1_012_1.fastq,/media/Fastq/Sample3_R1_013_1.fastq,/media/Fastq/Sample3_R1_014_1.fastq -2 /media/Fastq/Sample3_R2_001_2.fastq,/media/Fastq/Sample3_R2_002_2.fastq,/media/Fastq/Sample3_R2_003_2.fastq,/media/Fastq/Sample3_R2_004_2.fastq,/media/Fastq/Sample3_R2_005_2.fastq,/media/Fastq/Sample3_R2_006_2.fastq,/media/Fastq/Sample3_R2_007_2.fastq,/media/Fastq/Sample3_R2_008_2.fastq,/media/Fastq/Sample3_R2_009_2.fastq,/media/Fastq/Sample3_R2_010_2.fastq,/media/Fastq/Sample3_R2_011_2.fastq,/media/Fastq/Sample3_R2_012_2.fastq,/media/Fastq/Sample3_R2_013_2.fastq,/media/Fastq/Sample3_R2_014_2.fastq | /home//Biotools/sam/samtools view -S -b -o /media/RSEM_Map/Sample3_quals.temp/Sample3_quals.bam -" failed! Plase check if you provide correct parameters/options for the pipeline!

Any suggestions/comments on how to resolve this situation are most welcome.

P.S. Bowtie2 on its own is running fine.

Thanks
FlyWorker