Closed:cannot read data from simulated FASTQ files

Question

[anon]

Hi All,

after some suffering I realized, that perhaps my simulated paired-end fastq files are not correct in some way. (I found in Bowtie2 log 'no input read files were valid' and Trimmomatic couldn't handle these files either)

So, below there is a part of one of my paired end sequences, I don't know what's wrong with that:

@s_forw_0_1-17:0-81195210_1-5957-4/1
TCCCTCAGTTTCCCCATCTGTGAAATGGGCTGGCCATGCTTAACCCCTGGAGTTGCCAAGGTAGCCCATCAGGGAACACAGCGCCCCTGTACCTCAGGCACTCCC
+
??AA??B?DDD?D.DBGGCCCFIEIEHIIHIIIIIEIIHFHIGHIIHIHHIIIIIHIFFHIIHHHGHHIIHHHIIHHHFDI-IIHHHHIHCHHHIDIFHI,*HHH
@s_forw_0_1-17:0-81195210_1-5957-2/1
CCCTCAGTTTCCCCATCTGTGAAATGGGCTGGCCATGCTTAACCCCTGGAGTTGCCAAGGTAGCCCATCAGGGAACACAGCGCCCCTGTACCTCAGGCACTCCCT
+
?A???BBBDDADBDDBGGGGGGIIIFIHFHIIFHIHIDCHIFEIHIIGHIEGHDFGH+IHGIHHEC@5FEHIHHHIHH?IGFFIGHDHHIFIHHFHHGHIHCHHH
@s_revc_0_2-17:0-81195210_1-5957-4/1
GGGCGGGCTCAGGAAGAGGAGGCCAAGGACGGCCAAGAGAGGGGTGGGAGCAGGTGAGGACTGAGTGACCGTCCCGTCCAACAGGTGGACAAGACCGAAGACAAG
+
?????B?BBBDDEDDDFGGEGGHCHIHBHEHIIIHHIHHIIIHIHIHIHGIHEHHHHIHI==IIIFHHIIHHIAFAAIIHDIIGDHIHFHHGHFFHHIDFHHHGH
@s_revc_0_2-17:0-81195210_1-5957-2/1
GGTCACTCAGTCCTCACCTGCTCCCACCCCTCTCTTGGCCGTCCTTGGCCTCCTCTTCCTGAGCCCGCCCATCCGGCTGCTGCAGCCGGGCCTGGTCACGGTCCC
+
??AAABBBDDDDBDDEGGFCGFFIHFHIIIHHHFGGDFIICHHFIFFHDHHIIIHHIIIHHFIIHEEHHAFHHIHFIIH=GEIFIFHIIHHHIHHEHHHHHHFDH
@s_forw_1_1-17:0-81195210_1-5957-4/1
CAGGTGAGGACTGAGTGACCGTCCCGTCCAACAGGTGGACAAGACCGAAGACAAGTCCCTGGAGGAGCGGGGCCGCATCCTCATCTCGCTCAAGTACAGCTCACA
+
?,A??BBBBDDDBD@DFFGCFFIIIFIIFIIIIHIHHHIHHHHHFHIHIIIA=HIIIIIIHHICDHHHIHIFIHIEIHIH=HIBIH8HFIHHHGHHIG=HHI=HF
@s_forw_1_1-17:0-81195210_1-5957-2/1
CAGCTCACAGAAGCAAGGCCTGCTGGTAGGCATCGTGCGGTGCGCCCACCTGGCCGCCATGGACGCCAACGGCTACTCGGACCCCTACGTAAAAACGTGAGTGTG
+
??9??B?@DDDDDD6EGFGGGCHIB@ICICIIIIHHFIIIDHHIAHIIIHIHHFGIFIIIBHIIFHHHHHDHIHFIDIIIHHHCIII5HH+IAIHGHFHIHHGHH
@s_forw_1_2-17:0-81195210_1-5957-4/1
ACGGCACACTCACGTTTTCACGTAGGGGTCCGAGTAGCCGTTGGCGTCCATGGCGGCCAGGTGGGCGCACCGCACGATGCCTACCAGCAGGCCTTGCTTCTGTGA
+
?,????B?BBD-DDBDGGFGGCIAIHH/IFHHGAEIFIDHIIHHHIIHIF?HGIHIFIIFFHIHHIHIHHDHGHIIFH?IICGCII>EI.HIHCHIIHHHFH4HF
@s_forw_1_2-17:0-81195210_1-5957-2/1
GGTGCGCCCACCTGGCCGCCATGGACGCCAACGGCTACTCGGACCCCTACGTGAAAACGTGAGTGTGCCGTGCGCGTGACCACCTGCCACGTCTTCACCTCCAAG
+
????ABBBDDBDDDDDFCGGGFHHIIFHHIHIC=H9IEHHIIHGHIHICHHIHIFHIHIEHFIHFHHEHIHGHIHIICHIH@IAIIHIHFIIHIFHHHI=HHGDG
@s_forw_0_1-17:0-81195210_1-11156-4/1
CCCGATGAACTCATTGTGCCGGAATTTGTCCTCGTCACACACAGAGATCCTAGAGGGGGCGGTGGTGAGGGGCACAGCCAGTGCCTCAGACGCACTGGGCATGGT
+
?????B@BD@DDDDDDCGECFGIIFIFHIAIIHFEGIHFHHHFGIIHIIICCHIIIHIHFIEFHHHIGIIIFHIHHIDHHIHHHHFH#EIFDIHHFIGHHGFHHB
@s_forw_0_1-17:0-81195210_1-11156-2/1
CCTTCCTCACCTCCACCCCCTTGACTCTCCATGCTCACCTCCCCGGTCTCCCCTCCCCTCTCACTCTGCCCCTCATGAGTCCCATCACAGGCAGGAAGTTATGCC
+

the Trimmomatic command I used:

java -jar /opt/Trimmomatic-0.33/

trimmomatic-0.33.jar PE -trimlog ./fastq/Trimmomatic/trimlog_control_0_D1.txt ./fastq/control_0_D4_1.fq ./fastq/control_0_D4_2.fq ./fastq/Trimmomatic/Paired/control_0_D1_forward-paired.fastq ./fastq/Trimmomatic/Unpaired/control_0_D1_forward-unpaired.fastq ./fastq/Trimmomatic/Paired/control_0_D1_reverse-paired.fastq ./fastq/Trimmomatic/Unpaired/control_0_D1_reverse-unpaired.fastq ILLUMINACLIP:/opt/Trimmomatic-0.33/adapters/TruSeq3-PE.fa:2:40:10

and the output of it:

TrimmomaticPE: Started with arguments: -trimlog ./fastq/Trimmomatic/trimlog_control_0_D1.txt ./fastq/control_0_D4_1.fq ./fastq/control_0_D4_2.fq ./fastq/Trimmomatic/Paired/control_0_D1_forward-paired.fastq ./fastq/Trimmomatic/Unpaired/control_0_D1_forward-unpaired.fastq ./fastq/Trimmomatic/Paired/control_0_D1_reverse-paired.fastq ./fastq/Trimmomatic/Unpaired/control_0_D1_reverse-unpaired.fastq ILLUMINACLIP:/opt/Trimmomatic-0.33/adapters/TruSeq3-PE.fa:2:40:10
Multiple cores found: Using 4 threads
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Quality encoding detected as phred33
Input Read Pairs: 204352 Both Surviving: 204352 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully

Thank you for any help!