running SMuFin problems，can not read file?

[huic...@gmail.com]

[root@centos67 br]# mpirun --allow-run-as-root /tools/setup/smufin_0.9.3_mpi_beta/SMuFin --ref /ref/gatkhg19/hg19 --normal_fastq_1 /br/sfl_1.txt --normal_fastq_2 /br/sfl_2.txt --tumor_fastq_1 /br/sfm_1.txt --tumor_fastq_2 /br/sfm_2.txt --min_sup_reads 4 --cpus_per_node 2 --patient_id br
Checking input data files...
BWT index found for /ref/gatkhg19/hg19
It was not possible to read @ST-E00129:436:HGNH2CCXX:1:2213:8146:57477/1. Check if you entered the correct path to the file and you have the read permissions.
------------------------------------------
fastq file:
[root@centos67 br]# head sfl_1.txt
@ST-E00129:436:HGNH2CCXX:1:2213:8146:57477/1
GAGTGAGCAGTAGCAAGATTTATTGCAAAGAGTGAAAGAACGAAGCTTCCACAGTATGGAAAGGGACCCCATTGGGTTGCCACTGCTGGCTCAGGCAGTCTGCTTTTATTCTCTAATCTGCTCCCTCCCACATCCTGCTGATTGGTCCACT
+
AAFFFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK7FKKKAFKFFKFKKKKKKKKKKKKKFKKKKKKKKKKKKKKKKKFFKKKKKKKK
@ST-E00129:436:HGNH2CCXX:2:1213:14986:48757/1
ATCAGCAGGATGTGGGTGGTAGCAGATTAGAGAATAAAAGCAGACTGCCTGAGCCAGCAGTGGCAACCCAATGGGGTCCCTTTCCATCCTGTGGAAGCTTCGTTCTTTCCCTCTTTGCAATAAATCTTGCTATTGCTCACTCTTTGGGTCC
+
,AFFFKKKKKAFKFKAKKKKKKKKKKKKAFKKKKKKKFKKKKKKKKKKKKKKKKKKKKK7FK7FKKKKKKKKKKAFFKKKKKKKKKKAKKKKK,FFKKKKK,FKKKKKK,FKKKKKKKKKKKKKKKKK,FKKKKKKKKKKKKKKKKKKFKK
@ST-E00129:436:HGNH2CCXX:1:1212:25256:9589/1
CCTCACCCTCACCCTAACCCTAACCCTCACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTCACCCTAACCCTAACCCTAACCCTCACCCTAACCCTAACCCTAACCCCCACCCTCACCCTAACC
[root@centos67 br]# head sfl_2.txt
@ST-E00129:436:HGNH2CCXX:1:2213:8146:57477/2
CCTAACCCCAACCCTAACCCCAACCCCCACCCCCACCCCCCACCCCACCCCAACCCCCACCCCCACCCCACCCCCAACCCCCACCCCCACCCCCACCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCACCCCCCCCCCCCCAACCCCCA
+
AAFFFKKKK<KKKKFKKFKKK,FAKKF77(<FK<<(,FF<((,AA(A7(AF,7,7,F(,((A<(7(,AA,(,(<7<,,7AF,(,7A,(((,A<(((,(7((,((((,(FA(((,A<(((<AA,((,(,A(,(<(((((((<<((,,7<<((
@ST-E00129:436:HGNH2CCXX:2:1213:14986:48757/2
GACATATCTGTGTGGCCCATAGAGAGTAGATCCCAAAGACAGAAGGCCCAGGTCCCTAAACCCCCACAGGGGAACTGTGGTACAGACCAGGAGCTCATGTACAGGGCTGTCCCAGGGCCCCTAAAGTCCAGAAGGGAATTGGGCTAGAGAC
+
AAFFFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKKKKKFKFK,AFAFKKKKKKKK,AFK<AKFFKKFKKKKKKK,FAKFKKKKFKFAKKFAFAFKAFFKKKFFKKKKKAKKAAAFA7AAK,,AA7A<AAKFA,A,<7A,<AKKKA,
@ST-E00129:436:HGNH2CCXX:1:1212:25256:9589/2
TGTGGACCCAAAGAGTGAGCAATAGCAAGATTTATTGCAAAGAGTGAAAGAACGAAGCTTCCACAGTATGGAAAGGGACCCCATTGGGTTGCCACTGCTGGCTCAGGCAGTCTGCTTTTATTCTCTAATCTGCTACCACCCACATCCTGCT

can you help?
thanks

[SMuFin]

Hello,

You should have full permissions on the human reference folder. Can you run it with that?

Regards

[hamz...@gmail.com]

Hi,

I have a similar issue where the input sequence can't be read. The permissions for the reference file and folder and fastq files and folder are full (read write execute). The error still states "it was not possible to read @HS1_471:7:1101:1338:165306/1. Check if you entered the correct path to the file and you have the read permissions". I'm currently running it with smufin/0.9.3 and openMPI/1.8.1.

Is there anything else I can try to resolve this issue?

Regards,
Hamza Farooq