RunPipeline fails because "project dir does not exist"

RunPipeline command keeps failing, saying that project dir does not exist (even though the initPipeline completes and states that the directory was successfully created). I have used the initPipeline and runPipeline on the same server in the past, so I'm not sure what is going on now.

An example of the initPipeline: stevens.txbiomedgenetics.org% initPipeline -q -1 MicrobiomeDnaSeq_S17_L004_R1_001.fastq.gz -2 MicrobiomeDnaSeq_S17_L004_R2_001.fastq.gz -d 20170201_microbiome_test_S17 -i 200:800 Warning: BLASR is not found, some functionality will not be available Warning: Newbler is not found, some functionality will not be available Warning: MetaGeneMark is not found, some functionality will not be available Warning: SignalP+ is not found, some functionality will not be available Warning: metaphylerClassify is not found, some functionality will not be available Warning: PHmmer is not found, some functionality will not be available Warning: PhyloSift was not found, will not be available

Warning: EA-UTILS is not found, some functionality will not be available Warning: ALE is not found, some functionality will not be available Warning: CGAL is not found, some functionality will not be available Warning: REAPR is not found, some functionality will not be available Warning: FRCbam is not found, some functionality will not be available Warning: FreeBayes is not found, some functionality will not be available Warning: QUAST is not found, some functionality will not be available Warning: MPI is not available, some functionality may not be available Project dir /master/kreeves/metAMOS-1.5rc3/20170201_microbiome_test_S17 successfully created! Use runPipeline.py to start Pipeline

An example of the runPipeline: stevens.txbiomedgenetics.org% runPipeline –q –u –r –v –c kraken –a SOAPdenovo,soap,soap2,velvet,metavelvet,velvet-sc,spades,abyss,ray,edena,sga,masurca –t metamos –n Scaffold –f FunctionalAnnotation –z species –d 20170201_microbiome_test_S17 project dir does not exist! usage: runPipeline [options] -d projectdir -h = : print help [this message] -j = : just output all of the programs and citations then exit (default = NO) -v = : verbose output? (default = NO) -d = : directory created by initPipeline (REQUIRED)

[options]: [pipeline_opts] [misc_opts]

[pipeline_opts]: options that affect the pipeline execution Pipeline consists of the following steps: Preprocess, Assemble, FindORFS, MapReads, Abundance, Annotate, FunctionalAnnotation, Scaffold, Propagate, Classify, Postprocess Each of these steps can be referred to by the following options: -f = : force this step to be run (default = NONE) -s = : start at this step in the pipeline (default = Preprocess) -e = : end at this step in the pipeline (default = Postprocess) -n = : step to skip in pipeline (default=NONE)

For each step you can fine-tune the execution as follows [Preprocess] -t = : filter input reads? (default = metamos, supported = none,metamos,eautils,pbcr) -q = : produce FastQC quality report for reads with quality information (fastq or sff)? (default = NO) [Assemble] -a = : genome assembler to use (default = soapdenovo, supported = newbler,soapdenovo,soapdenovo2,ca,velvet,velvet-sc,metavelvet,metaidba,sparseassembler,minimus,abyss,edena,spades,mira,sga,idba-ud,ray,masurca) -k = : k-mer size to be used for assembly (default = 31) -o = >: min overlap length [MapReads] -m = : read mapper to use? (default = bowtie, supported = bowtie,bowtie2) -i = : save bowtie (i)ndex? (default = NO) -b = : create library specific per bp coverage of assembled contigs (default = NO) [FindORFS] -g = : gene caller to use (default = fraggenescan, supported = fraggenescan,metagenemark,glimmermg) -l = : min contig length to use for ORF call (default = 300) -x = >: min contig coverage to use for ORF call (default = 3X) [Validate] -X = : comma-separated list of validators to run on the assembly. (default = lap, supported = reapr,orf,lap,ale,quast,frcbam,freebayes,cgal,n50) -S = : comma-separated list of scores to use to select the winning assembly. By default, all validation tools specified by -X will be run. For each score, an optional weight can be specified as SCORE:WEIGHT. For example, LAP:1,CGAL:2 (supported = all,lap,ale,cgal,snp,frcbam,orf,reapr,n50) [Annotate] -c = : classifier to use for annotation (default = kraken, supported = fcp,phylosift,phmmer,blast,metaphyler,phymm,kraken -u = : annotate unassembled reads? (default = NO) [Classify] -z = : taxonomic level to categorize at (default = class)

[misc_opts]: Miscellaneous options -B = : blast DBs not available (default = NO) -r = : retain the AMOS bank? (default = NO) -p = : number of threads to use (be greedy!) (default=1) -4 = : 454 data? (default = NO) -L = : generate local Krona plots. Local Krona plots can only be viewed on the machine they are generated on but will work on a system with no internet connection (default = NO) stevens.txbiomedgenetics.org% runPipeline –q –u –r –v –c kraken –t metamos –n Scaffold –f FunctionalAnnotation –z species –d 20170201_microbiome_test_S17 project dir does not exist! usage: runPipeline [options] -d projectdir -h = : print help [this message] -j = : just output all of the programs and citations then exit (default = NO) -v = : verbose output? (default = NO) -d = : directory created by initPipeline (REQUIRED)

[options]: [pipeline_opts] [misc_opts]

Any help or guidance will be appreciated!

Thanks, Kim

marbl / metAMOS

RunPipeline fails because "project dir does not exist" #259