running error when using mm10

[Feizhen Wu]

Hi Bo,

When I run below commands:

      bowtie2 -p 20 -x mm10_Bowtie2Index/genome -1 R1.fq -2 R2.fq -S test.sam &

      samtools view -Sb test.sam > test.sam.bam

      samtools sort test.sam.bam test.sam_sorted

      samtools index test.sam_sorted.bam

      trust -f test.sam_sorted.bam -g mm10 -n 10

and found error message below:

Please install parasail. If not, use BioPython instead.

        ===================================================================

        Tcr Repertoire Utilities for Solid Tissue, or TRUST, is a toolbox

        for analyzing T and B cell receptors in solid tumors using unselected

        RNA-seq data. TRUST performs de novo assembly of informative unmapped

        reads to estimate the TCR transcripts. It also estimates the CDR3 

        sequences and the relative fractions of different T or B cell 

        clonotypes.

        ===================================================================

        

----- Run TCR analysis -----

test.sam_sorted.bam

Screen for informative reads

['chr6', '40891296', '41558371', 'TRB']

['chr14', '52427967', '54224198', 'TRA']

['chr13', '19178042', '19352343', 'TRG']

Pair reads in the region

--processed 1000000 reads

--processed 2000000 reads

--processed 3000000 reads

--processed 4000000 reads

('Read length:', 150)

ScreenGenome Finished! sr =  0

Total reads extracted 35

Informative read pairs kept 6

Paired-end mode

---Processing TRAV13N-4|chr14:53362368-53364106.

Reads: 1

Contigs: 0

---Processing TRBC2|chr6:41546730-41548181.

Reads: 2

Contigs: 0

---Processing TRAC|chr14:54220521-54224198.

Reads: 2

Contigs: 2

---Processing TRBV1|chr6:40891296-40891885.

Reads: 1

Contigs: 1

PE: GetReadsOverlapByGene, FindDisjointCommunities, AssembleCommReads ...time elapsed 0.004338

PE: MergeMasterContig...time elapsed 0.000151

Final contigs assembled 3

PE: AnnotateCDR3...time elapsed 0.185921

Process unmapped read pairs

# Extract reads with joining gene DNA motif

1000000

48

Traceback (most recent call last):

  File "/opt/anaconda/bin/trust", line 4, in <module>

    __import__('pkg_resources').run_script('trust==3.0.2', 'trust')

  File "/opt/anaconda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 654, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/opt/anaconda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1434, in run_script

    exec(code, namespace, namespace)

  File "/home/wfz/.local/lib/python2.7/site-packages/trust-3.0.2-py2.7-linux-x86_64.egg/EGG-INFO/scripts/trust", line 18, in <module>

    main()

  File "/home/wfz/.local/lib/python2.7/site-packages/trust-3.0.2-py2.7-linux-x86_64.egg/EGG-INFO/scripts/trust", line 14, in main

    trust_main(opt)

  File "/home/wfz/.local/lib/python2.7/site-packages/trust-3.0.2-py2.7-linux-x86_64.egg/trust/trust_main.py", line 252, in trust_main

    annListU,ContigFinalListU=ProcessSingleEndReads(ffu,LocusFile,HeavyChain=HC,light_chain=light_chain,err=Err,overlap_thr=thr_L,fasta=fasta,unmapped=True,Bcell=Bcell, genome=ReferenceGenome)

  File "/home/wfz/.local/lib/python2.7/site-packages/trust-3.0.2-py2.7-linux-x86_64.egg/trust/single_end_mode.py", line 345, in ProcessSingleEndReads

    pat=re.compile(pp)

  File "/opt/anaconda/lib/python2.7/re.py", line 194, in compile

    return _compile(pattern, flags)

  File "/opt/anaconda/lib/python2.7/re.py", line 251, in _compile

    raise error, v # invalid expression

sre_constants.error: nothing to repeat

Could you let me know where the problem?

Many thanks.

Best,

Feizhen Wu