bwa mem invalid option in HERA pipeline

[shiyi-pan]

Hi, I run the HERA using test data and got an error about bwa mem. I run the code below and got an 1.pbs file, perl $Working_Script/09-Qsub-Pair_Alignment.pl list_outer_pacbio.txt $Working_Script $queue $genome_name >>log

here is 1.pbs file,

BSUB -J Test-Pair-0-0

BSUB -o 1.out

BSUB -n 4

BSUB -q normal

bwa mem -a -e -t 4 ./03-Pacbio-SelfAlignment/Both_Side_Pacbio.part-1.fasta ./03-PacbioSelfAlignment/Both_Side_Pacbio.part-1.fasta >./03-Pacbio-SelfAlignment/Part_SelfAlignment_0-0.sam perl /gss1/home/hjb20181119/panyongpeng/NN1138-2/genome_assembly/HERA/HERA//sam2blasr.pl ./03-PacbioSelfAlignment/Part_SelfAlignment_0-0.sam ./03-Pacbio-SelfAlignment/Part_SelfAlignment_0-0.txt rm -f ./03-Pacbio-SelfAlignment/Part_SelfAlignment_0-0.sam

I run "bwa mem -a -e -t 4 ./03-Pacbio-SelfAlignment/Both_Side_Pacbio.part-1.fasta ./03-PacbioSelfAlignment/Both_Side_Pacbio.part-1.fasta >./03-Pacbio-SelfAlignment/Part_SelfAlignment_0-0.sam" and got an error: mem: invalid option -- 'e'.

I checked the bwa mem option list by type 'bwa mem' on the command line and there is no 'e' option indeed:

Usage: bwa mem [options] [in2.fq]

Algorithm options:

   -t INT        number of threads [1]
   -k INT        minimum seed length [19]
   -w INT        band width for banded alignment [100]
   -d INT        off-diagonal X-dropoff [100]
   -r FLOAT      look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]
   -y INT        seed occurrence for the 3rd round seeding [20]
   -c INT        skip seeds with more than INT occurrences [500]
   -D FLOAT      drop chains shorter than FLOAT fraction of the longest overlapping chain [0.50]
   -W INT        discard a chain if seeded bases shorter than INT [0]
   -m INT        perform at most INT rounds of mate rescues for each read [50]
   -S            skip mate rescue
   -P            skip pairing; mate rescue performed unless -S also in use

Scoring options:

   -A INT        score for a sequence match, which scales options -TdBOELU unless overridden [1]
   -B INT        penalty for a mismatch [4]
   -O INT[,INT]  gap open penalties for deletions and insertions [6,6]
   -E INT[,INT]  gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [1,1]
   -L INT[,INT]  penalty for 5'- and 3'-end clipping [5,5]
   -U INT        penalty for an unpaired read pair [17]

   -x STR        read type. Setting -x changes multiple parameters unless overridden [null]
                 pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0  (PacBio reads to ref)
                 ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0  (Oxford Nanopore 2D-reads to ref)
                 intractg: -B9 -O16 -L5  (intra-species contigs to ref)

Input/output options:

   -p            smart pairing (ignoring in2.fq)
   -R STR        read group header line such as '@RG\tID:foo\tSM:bar' [null]
   -H STR/FILE   insert STR to header if it starts with @; or insert lines in FILE [null]
   -o FILE       sam file to output results to [stdout]
   -j            treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)
   -5            for split alignment, take the alignment with the smallest coordinate as primary
   -q            don't modify mapQ of supplementary alignments
   -K INT        process INT input bases in each batch regardless of nThreads (for reproducibility) []

   -v INT        verbosity level: 1=error, 2=warning, 3=message, 4+=debugging [3]
   -T INT        minimum score to output [30]
   -h INT[,INT]  if there are <INT hits with score >80% of the max score, output all in XA [5,200]
   -a            output all alignments for SE or unpaired PE
   -C            append FASTA/FASTQ comment to SAM output
   -V            output the reference FASTA header in the XR tag
   -Y            use soft clipping for supplementary alignments
   -M            mark shorter split hits as secondary

   -I FLOAT[,FLOAT[,INT[,INT]]]
                 specify the mean, standard deviation (10% of the mean if absent), max
                 (4 sigma from the mean if absent) and min of the insert size distribution.
                 FR orientation only. [inferred]

Note: Please read the man page for detailed description of the command line and options.

Is my bwa version wrong ? could you help me fix this error ? thank you very much.

[whc2]

bwa (v0.7.12-r1039) can be used.