TrackDb.txt sample group indentation

[fwzhao]

TrackDb.txt sample group indentation error leads to
needLargeMem: trying to allocate 0 bytes

[afrendeiro]

needLargeMem: trying to allocate 0 bytes <- occurs in UCSC browser.

Also related, trackmanager should remove groups with no attributes set to avoid for example:

subGroup3 ip ip \
    = \  <- this "group" shouldn't be added
    H3K27ac=H3K27ac \
    IgG=IgG \
    Input=Input

[afrendeiro]

@fwzhao please test with latest master branch or commit b525182

[fwzhao]

Tested with ngstk version 0.1.3.6, same issue arises again

[afrendeiro]

Can you post a sample of trackDb.txt with the problematic part? (or simply send me the link to it)

[fwzhao]

I think it has to do with multiWig containers for replicated samples (and it's indentation). My current workaround is to get rid of all multiWigs, and reassign parents. Example requested below -

---

track omni_atac
container multiWig
shortLabel variations of omni-atac protocol (Greenleaf lab)
longLabel variations of omni-atac protocol (Greenleaf lab)
container multiWig
aggregate none
showSubtrackColorOnUi on
type bigWig
autoScale on
visibility full
maxHeighPixels 32:32:8
subGroup1 protocol protocol \
    ATACseq_Omni_Greenleaf=ATACseq_Omni_Greenleaf \
    ATACseq_Omni_test-v1=ATACseq_Omni_test-v1 \
    ATACseq_Omni_test-v2=ATACseq_Omni_test-v2 \
    ATACseq_v2_fz=ATACseq_v2_fz \
    fastATAC4=fastATAC4 \
    omniATAC1=omniATAC1 \
    omniATAC1_omniATAC1=omniATAC1_omniATAC1
subGroup2 protocol_general protocol_general \
    fastATAC=fastATAC \
    omni_ATAC=omni_ATAC
subGroup3 cell_type cell_type \
    Jurkat=Jurkat \
    KMM1=KMM1 \
    M579=M579 \
    M579-TIL209=M579-TIL209
subGroup4 cell_count cell_count \
    50k=50k \
    50k-30k=50k-30k \
    5k=5k
sortOrder protocol=+ protocol_general=+ cell_type=+ cell_count=+
dimensions dimX=protocol dimY=protocol_general dimABCDEFGHIJKLMNOPQRSTUVW=cell_type

    track omniATAC1_omni_ATAC_M579_50k
    shortLabel omniATAC1 omni_ATAC M579 50k
    longLabel omniATAC1 omni_ATAC M579 50k
    parent omni_atac
    container multiWig
    aggregate transparentOverlay
    showSubtrackColorOnUi on
    type bigWig
    visibility full
    maxHeighPixels 32:32:8
        subGroups protocol=omniATAC1 protocol_general=omni_ATAC cell_type=M579 cell_count=50k

        track M579_omniATAC1_CS_50k_customTn5_FACS_r1
        shortLabel M579_omniATAC1_CS_50k_customTn5_FACS_r1
        longLabel M579_omniATAC1_CS_50k_customTn5_FACS_r1
        parent omniATAC1_omni_ATAC_M579_50k
        type bigWig
        graphTypeDefault bar
        visibility full
        height 32
        maxHeighPixels 32:32:8
        windowingFunction mean
        autoScale on
        bigDataUrl M579_omniATAC1_CS_50k_customTn5_FACS_r1.bigWig
        color 205,255,0
        subGroups protocol=omniATAC1 protocol_general=omni_ATAC cell_type=M579 cell_count=50k


        track M579_omniATAC1_CS_50k_illuminaTn5_FACS_r1
        shortLabel M579_omniATAC1_CS_50k_illuminaTn5_FACS_r1
        longLabel M579_omniATAC1_CS_50k_illuminaTn5_FACS_r1
        parent omniATAC1_omni_ATAC_M579_50k
        type bigWig
        graphTypeDefault bar
        visibility full
        height 32
        maxHeighPixels 32:32:8
        windowingFunction mean
        autoScale on
        bigDataUrl M579_omniATAC1_CS_50k_illuminaTn5_FACS_r1.bigWig
        color 205,255,0
        subGroups protocol=omniATAC1 protocol_general=omni_ATAC cell_type=M579 cell_count=50k


track M579-TIL209_omniATAC1_omniATAC1_CS_50k-30k_customTn5-customTn5_NoFACS-FACS_r1
shortLabel M579-TIL209_omniATAC1_omniATAC1_CS_50k-30k_customTn5-customTn5_NoFACS-FACS_r1
longLabel M579-TIL209_omniATAC1_omniATAC1_CS_50k-30k_customTn5-customTn5_NoFACS-FACS_r1
parent omni_atac
type bigWig
graphTypeDefault bar
visibility full
height 32
maxHeighPixels 32:32:8
windowingFunction mean
autoScale on
bigDataUrl M579-TIL209_omniATAC1_omniATAC1_CS_50k-30k_customTn5-customTn5_NoFACS-FACS_r1.bigWig
color 255,0,40
subGroups protocol=omniATAC1_omniATAC1 protocol_general=omni_ATAC cell_type=M579-TIL209 cell_count=50k-30k