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Understanding IRMA output

Output for IRMA is deposited into the working directory of the calling user as a new subfolder. This subfolder is named using the sample name argument. If the subfolder already exists with the same name, IRMA will add a suffix in the format of "-V#", incrementing the number until it finds a folder that doesn't exist. Below is typical output from a sample in our manuscript, but we have excluded all gene segments except A_MP for brevity. Hover over underlined text for an explanation of the output file or folder; click on links under the figures/ and tables/ folder to see output samples and explanations.


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IRMA output directory structure (only showing A_MP)

Mixture_Example/Sample name
├── amended_consensus/Assembled consensuses per gene segment w/mixed base calls.
│   └── Mixture_Example_7.fa
├── figures/
│   ├── A_MP-coverageDiagram.pdfShows coverage and variant calls.
│   ├── A_MP-heuristics.pdfHeuristic graphs for A_MP
│   ├── A_MP-EXPENRD.pdfA_MP variant phasing using 'experimental enrichment" distances
│   ├── A_MP-JACCARD.pdfA_MP variant phasing using modified Jaccard distances
│   ├── A_MP-MUTUALD.pdfA_MP variant phasing using mutual association distances
│   ├── A_MP-NJOINTP.pdfA_MP variant phasing using normalized joint probability distances
│   └── READ_PERCENTAGES.pdfBreak down for reads assembled.
├── intermediate/Intermediate data for each step
│   ├── 0-ITERATIVE-REFERENCES/
│   │   ├── R0-A_MP.refStarting reference library sequence for A_MP
│   │   ├── R1-A_MP.refWorking reference for A_MP after round 1, template for round 2
│   │   └── R2-A_MP.refWorking reference for A_MP after round 2
│   ├── 1-MATCH_BLAT/
│   │   ├── R1.tar.gz
│   │   ├── R2.tar.gzArchive of BLAT results for the MATCH step.
│   │   └── R3.tar.gz
│   ├── 2-SORT_BLAT/
│   │   ├── R1.tar.gzClassification/sorting intermediate files for round 1
│   │   ├── R1.txtSummary statistics of sorting results for round 1
│   │   ├── R2.tar.gz
│   │   └── R2.txt
│   ├── 3-ALIGN_SAM/
│   │   └── storedCounts.tar.gzStatistic files used to create rough assembly consensus sequences
│   └── 4-ASSEMBLE_SSWFinal assembly phase intermediate iterative resuls
│       ├── F1-A_MP.bamUnsorted BAM file for A_MP assembly, iteration 1
│       ├── F1-A_MP.refReference for final assembly, A_MP, iteration 1
│       ├── F2-A_MP.bam
│       ├── F2-A_MP.ref
│       └── reads.tar.gzArchive of sorted, unmerged reads by gene segment
├── logs/
│   ├── ASSEMBLY_log.txtSSW scores per all rounds tried in the iterative refinement
│   ├── NR_COUNTS_log.txtRead pattern counts at various stages
│   ├── QC_log.txtQuality control output
│   ├── READ_log.txtCounts of assembled reads from BAM files
│   ├── FLU-Mixture_Example.shConfiguration file corresponding to this IRMA run
│   └── run_info.txtTable of parameters used by the IRMA run
├── matrices/Phasing matrices used to generate heat maps
│   ├── A_MP-EXPENRD.sqm
│   ├── A_MP-JACCARD.sqm
│   ├── A_MP-MUTUALD.sqm
│   └── A_MP-NJOINTP.sqm
├── secondary/
│   ├── R1-A_NA_N1.faTrace A_NA_N1 sorted into secondary status
│   ├── R1-UNRECOGNIZABLE.faRead patterns that matched flu but had poor signal according to LABEL
│   ├── R2-UNRECOGNIZABLE.fa
│   └── unmatched_read_patterns.tar.gzArchive of left over read patterns that did not match FLU
├── tables/

│   ├── A_MP-pairingStats.txtSummary of paired-end merging statistics, if applicable, A_MP
│   ├── A_MP-coverage.txtSummary coverage statistics for the assembly, A_MP
│   ├── A_MP-allAlleles.txtStatistics for every position & allele in the assembly, A_MP
│   ├── A_MP-insertions.txtCalled insertion variants for A_MP
│   ├── A_MP-deletions.txtCalled deletion variants for A_MP
│   ├── A_MP-variants.txtCalled single nucleotide variants for A_MP
│   └── READ_COUNTS.txtRead counts for various points in the assembly process
├── A_MP.bamSorted BAM file for the final A_MP assembly (merged if applicable)
├── A_MP.bam.baiBAM file index for A_MP assembly
├── A_MP.fastaFinal assembled plurality consensus (no mixed base calls) for A_MP
└── A_MP.vcfCustom variant call file for called IRMA variants, A_MP




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This page last reviewed: Friday, November 04, 2016
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