A5-miseq pipeline error

Question

[endihur98]

Hi! I'm trying to make an assemble using the A5-miseq pipeline, but I encounter these errors:

(qiime2-2020.2) root@Enrique:/mnt/c/Users/endih/Desktop/prueba# ./../a5_miseq_linux_20160825/bin/a5_pipeline.pl ./../a5_miseq_linux_20160825/example/phiX_p1.fastq ./../a5_miseq_linux_20160825/example/phiX_p2.fastq  Test_Results
[a5] Found the following libraries:
     raw1:
      id=raw1
      p1=./../a5_miseq_linux_20160825/example/phiX_p1.fastq
      p2=./../a5_miseq_linux_20160825/example/phiX_p2.fastq
[a5] Found 1 libraries
[a5] Starting pipeline at step 1
[a5] Cleaning reads with SGA
[a5] Cleaning reads with SGA
cleaning each PE lib

p1 is ./../a5_miseq_linux_20160825/example/phiX_p1.fastq
Cleaning reads

[a5] java -Xmx512m -jar '/mnt/c/Users/endih/Desktop/a5_miseq_linux_20160825/bin'/trimmomatic.jar SE -threads 4 -phred64  Test_Results.s1/phiX_p1.fastq.both.fastq Test_Results.s1/phiX_p1.fastq.trim.fastq ILLUMINACLIP:/mnt/c/Users/endih/Desktop/a5_miseq_linux_20160825/bin/../adapter.fasta:2:30:10
LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
TrimmomaticSE: Started with arguments: -threads 4 -phred64 Test_Results.s1/phiX_p1.fastq.both.fastq Test_Results.s1/phiX_p1.fastq.trim.fastq ILLUMINACLIP:/mnt/c/Users/endih/Desktop/a5_miseq_linux_20160825/bin/../adapter.fasta:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'TCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'
Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GCCTTGCCAGCCCGCTCAGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGA'
Using Long Clipping Sequence: 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using Long Clipping Sequence: 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCTGATGGCGCGAGGGAGGC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCTGAGCGGGCTGGCAAGGC'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
Using Long Clipping Sequence: 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA'
Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'
ILLUMINACLIP: Using 3 prefix pairs, 16 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Reads: 6400 Surviving: 6371 (99.55%) Dropped: 29 (0.45%)
TrimmomaticSE: Completed successfully
[a5] '/mnt/c/Users/endih/Desktop/a5_miseq_linux_20160825/bin'/sga preprocess -q 25 -f 20 -m 35  --pe-mode=0 --phred64  Test_Results.s1/phiX_p1.fastq.trim.fastq > Test_Results.s1/phiX_p1.fastq.both.pp 2> /dev/null
[a5] sga index -d 1466142 -t 4 Test_Results.s1/Test_Results.pp.fastq > Test_Results.s1/index.out 2> Test_Results.s1/index.err
[a5] sga index -d 733071 -t 4 Test_Results.s1/Test_Results.pp.fastq > Test_Results.s1/index.out 2> Test_Results.s1/index.err
[a5] '/mnt/c/Users/endih/Desktop/a5_miseq_linux_20160825/bin'/sga correct -t 4 -p Test_Results.pp -o Test_Results.s1/phiX_p1.fastq.both.pp.ec.fastq
Test_Results.s1/phiX_p1.fastq.both.pp > Test_Results.s1/raw1.correct.out

> Error: could not open Test_Results.pp.bwt for read

readline() on closed filehandle TDPIPE at ./../a5_miseq_linux_20160825/bin/a5_pipeline.pl line 503.
Running cat Test_Results.s1/phiX_p1.fastq.both.repair.fastq >> Test_Results.s1/Test_Results.ec.fastq
Done merging libraries

> [a5] ERROR: Unable to identify any properly paired reads

> [a5] ERROR: Please check that you have provided at least one library of paired-end reads with names conforming to the Illumina read pair convent

Could someone help me with the errors, please?