Error: reads file does not look like a FASTQ file

[jtamames]

Hello
I am working with some CAMI dataset consisting in simulated reads from a mock community.
Bowtie2 does not recognize the reads as valid fastq, even if they are and ran successfully in a previous assembly step.
The command is:
bowtie2 -x /home/tamames/marinemags/bintest/sample0/data/sample0.bowtie -1 sample0.sample0.current_1.gz -2 sample0.sample0.current_2.gz --quiet -p 12 -S sample0.sample0.sam --very-sensitive-local

which fails with:

 Aligning to reference with bowtie
Error: reads file does not look like a FASTQ file
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134

The read files looks good to me, as proper fastq files:
zcat sample0.sample0.current_1.gz

>@S0R0
TCACCCGGCCGACGGGCAGATCGCACCTGATGCCCTATCGCTCCCTTGGCAAATTGAACCGGTTATAGGCGATAGCAAAGAGATAATTTTTGGCCAATGGGC
AAGAGATCTAGGTGCAAAAGTAGAAGGGCGACAAGTATCCAGCTCGAA
+
DDAEEEGGIII@IKJKKHKKKKJKKHKKHJJKHKCIK>EKHJKEICKHFIEKEJIK6EJE.DCEKDFKEIEFEE,IEIEGEEFFEEEE$EF4E?DED)EEEE
ECEECDEED=EC)?EFEEEEFDEBCCCA;AEEEEAE@EEE$A$$DF'?
>@S0R1
CGGAAATTTATAAATTTGCGTCTAATCCGGGCAGCTACAGACTGTTCTCTAGTGACAGCAGAGCGGCCGATTTCTCGGTTTCGGGAGACCTCCGTTTCGGTG
CTATCACCGACGAGACGGGTCAACTGCTAGTCATCGATTTGGCGTCCG
+
DD;GGGGCIIIIIKJJAKIKHKJKIKKGEEKKKKFKKK1HJK@AJIHJ=JDEGJKKEJ<GK5DE$EEHEEAKBC=FEEEFDE@EE$EFEEEEEE@ECEEE6E
EB$E;ECEEEDEDEE=EDEB?E7CDC$:$/EEBECDEE6?BD$ECE';

zcat sample0.sample0.current_2.gz

>@S0R0
TGGCAATCACAGCGGATACTTTCGCTACATCGTGAGCACCAGCCCACGGCAAGATGGCTTGCTTGCGATCAACCCCTTGGTGGGAGAGCCAACTTTTCGCGC
TGGATACTTGTCGCCCTTCTCCTTTTGCACCTAGTTCTCTTGCCCATT
+
DDAGEEEGIICI$KJKKKKAKJKKKK4IKDKKK?KFF<7KKCJKB:GKK:$JFKHDJHIIJEFHFD$JE9FCCD$EEEDDEE=6CED?D;FCEE/DK:CD@9
EDDE$EACAEED$=?CCEDB$AF)EF?)CD?9$E$$E?C$:AC;DEE$
>@S0R1
GTTACAGCGCCGGTATCCACAGAAATTTTCGACAGTTTCTCCTGCTTGTCTCCCTGGATAAAATAGATGGTCTTGCCGTCAACCGACCAAGTCAGATCCGTC
TTGACGCTGGAATCCTTGGCAAGCGGCTCTACCGCTCCGGACGCCAAA
+
A<DGGG;GG@IGEJ3KJJCFIHJKKJKJIKKKKJIKHI=JJJKKCKEJFGJJJEFIK@>DKK@IEEEG<EDECAEE<F?EC$C9DEEDIFEFEFECEC:EFD
D@EEEEEEC$$E=CD$ED$EDED@?;EC$DFCEEADC1D$=DDC$4CE

Any help would be greatly appreciated.
Best,
J

[ch4rr0]

Hello,

FASTQ headers start with a @ while FASTA's begin with a >. Also make sure that your sequence and qaulities are all on one line. Bowtie2 does not (yet) handle these fields being split across multiple lines. Hope this helps.