Clodius process killed when converting bigWig to hitile
Closed this issue · 1 comments
alexpreynolds commented
In preparation for ingesting bigWig signal tracks, I tried converting a test bigWig file to hitile format using conda (Python v3.6.4) and clodius v0.7.4. The host is a t2.micro EC2 instance running Ubuntu Xenial v16.04.
The aggregation proceeds up to the point of processing chr1 and the process is then killed.
The file /tmp/LN43287.75_20.normalized.GRCh38_no_alts.bw is a bigWig file containing DNase I density signal. I can make this available privately, if useful.
Here is the log of my conversion attempt:
$ clodius aggregate bigwig /tmp/LN43287.75_20.normalized.GRCh38_no_alts.bw \
--output-file /tmp/LN43287.75_20.normalized.GRCh38_no_alts.bw.hitile \
--assembly hg38
there
chrom_order: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chrM', 'chr15_KI270905v1_alt', 'chr6_GL000256v2_alt', 'chr6_GL000254v2_alt', 'chr6_GL000251v2_alt', 'chr6_GL000253v2_alt', 'chr6_GL000250v2_alt', 'chr6_GL000255v2_alt', 'chr6_GL000252v2_alt', 'chr17_KI270857v1_alt', 'chr16_KI270853v1_alt', 'chr16_KI270728v1_random', 'chr17_GL000258v2_alt', 'chr5_GL339449v2_alt', 'chr14_KI270847v1_alt', 'chr17_KI270908v1_alt', 'chr14_KI270846v1_alt', 'chr5_KI270897v1_alt', 'chr7_KI270803v1_alt', 'chr19_GL949749v2_alt', 'chr19_KI270938v1_alt', 'chr19_GL949750v2_alt', 'chr19_GL949748v2_alt', 'chr19_GL949751v2_alt', 'chr19_GL949746v1_alt', 'chr19_GL949752v1_alt', 'chr8_KI270821v1_alt', 'chr1_KI270763v1_alt', 'chr6_KI270801v1_alt', 'chr19_GL949753v2_alt', 'chr19_GL949747v2_alt', 'chr8_KI270822v1_alt', 'chr4_GL000257v2_alt', 'chr12_KI270904v1_alt', 'chr4_KI270925v1_alt', 'chr15_KI270852v1_alt', 'chr15_KI270727v1_random', 'chr9_KI270823v1_alt', 'chr15_KI270850v1_alt', 'chr1_KI270759v1_alt', 'chr12_GL877876v1_alt', 'chrUn_KI270442v1', 'chr17_KI270862v1_alt', 'chr15_GL383555v2_alt', 'chr19_GL383573v1_alt', 'chr4_KI270896v1_alt', 'chr4_GL383528v1_alt', 'chr17_GL383563v3_alt', 'chr8_KI270810v1_alt', 'chr1_GL383520v2_alt', 'chr1_KI270762v1_alt', 'chr15_KI270848v1_alt', 'chr17_KI270909v1_alt', 'chr14_KI270844v1_alt', 'chr8_KI270900v1_alt', 'chr10_GL383546v1_alt', 'chr13_KI270838v1_alt', 'chr8_KI270816v1_alt', 'chr22_KI270879v1_alt', 'chr8_KI270813v1_alt', 'chr11_KI270831v1_alt', 'chr15_GL383554v1_alt', 'chr8_KI270811v1_alt', 'chr18_GL383567v1_alt', 'chrX_KI270880v1_alt', 'chr8_KI270812v1_alt', 'chr19_KI270921v1_alt', 'chr17_KI270729v1_random', 'chr17_JH159146v1_alt', 'chrX_KI270913v1_alt', 'chr6_KI270798v1_alt', 'chr7_KI270808v1_alt', 'chr22_KI270876v1_alt', 'chr15_KI270851v1_alt', 'chr22_KI270875v1_alt', 'chr1_KI270766v1_alt', 'chr19_KI270882v1_alt', 'chr3_KI270778v1_alt', 'chr15_KI270849v1_alt', 'chr4_KI270786v1_alt', 'chr12_KI270835v1_alt', 'chr17_KI270858v1_alt', 'chr19_KI270867v1_alt', 'chr16_KI270855v1_alt', 'chr8_KI270926v1_alt', 'chr5_GL949742v1_alt', 'chr3_KI270780v1_alt', 'chr17_GL383565v1_alt', 'chr2_KI270774v1_alt', 'chr4_KI270790v1_alt', 'chr11_KI270927v1_alt', 'chr19_KI270932v1_alt', 'chr11_KI270903v1_alt', 'chr2_KI270894v1_alt', 'chr14_GL000225v1_random', 'chrUn_KI270743v1', 'chr11_KI270832v1_alt', 'chr7_KI270805v1_alt', 'chr4_GL000008v2_random', 'chr7_KI270809v1_alt', 'chr19_KI270887v1_alt', 'chr4_KI270789v1_alt', 'chr3_KI270779v1_alt', 'chr19_KI270914v1_alt', 'chr19_KI270886v1_alt', 'chr11_KI270829v1_alt', 'chr14_GL000009v2_random', 'chr21_GL383579v2_alt', 'chr11_JH159136v1_alt', 'chr19_KI270930v1_alt', 'chrUn_KI270747v1', 'chr18_GL383571v1_alt', 'chr19_KI270920v1_alt', 'chr6_KI270797v1_alt', 'chr3_KI270935v1_alt', 'chr17_KI270861v1_alt', 'chr15_KI270906v1_alt', 'chr5_KI270791v1_alt', 'chr14_KI270722v1_random', 'chr16_GL383556v1_alt', 'chr13_KI270840v1_alt', 'chr14_GL000194v1_random', 'chr11_JH159137v1_alt', 'chr19_KI270917v1_alt', 'chr7_KI270899v1_alt', 'chr19_KI270923v1_alt', 'chr10_KI270825v1_alt', 'chr19_GL383576v1_alt', 'chr19_KI270922v1_alt', 'chrUn_KI270742v1', 'chr22_KI270878v1_alt', 'chr19_KI270929v1_alt', 'chr11_KI270826v1_alt', 'chr6_KB021644v2_alt', 'chr17_GL000205v2_random', 'chr1_KI270765v1_alt', 'chr19_KI270916v1_alt', 'chr19_KI270890v1_alt', 'chr3_KI270784v1_alt', 'chr12_GL383551v1_alt', 'chr20_KI270870v1_alt', 'chrUn_GL000195v1', 'chr1_GL383518v1_alt', 'chr22_KI270736v1_random', 'chr10_KI270824v1_alt', 'chr14_KI270845v1_alt', 'chr3_GL383526v1_alt', 'chr13_KI270839v1_alt', 'chr22_KI270733v1_random', 'chrUn_GL000224v1', 'chr10_GL383545v1_alt', 'chrUn_GL000219v1', 'chr5_KI270792v1_alt', 'chr17_KI270860v1_alt', 'chr19_GL000209v2_alt', 'chr11_KI270830v1_alt', 'chr9_KI270719v1_random', 'chrUn_GL000216v2', 'chr22_KI270928v1_alt', 'chr1_KI270712v1_random', 'chr6_KI270800v1_alt', 'chr1_KI270706v1_random', 'chr2_KI270776v1_alt', 'chr18_KI270912v1_alt', 'chr3_KI270777v1_alt', 'chr5_GL383531v1_alt', 'chr3_JH636055v2_alt', 'chr14_KI270725v1_random', 'chr5_KI270796v1_alt', 'chr9_GL383541v1_alt', 'chr19_KI270885v1_alt', 'chr19_KI270919v1_alt', 'chr19_KI270889v1_alt', 'chr19_KI270891v1_alt', 'chr19_KI270915v1_alt', 'chr19_KI270933v1_alt', 'chr19_KI270883v1_alt', 'chr19_GL383575v2_alt', 'chr19_KI270931v1_alt', 'chr12_GL383550v2_alt', 'chr13_KI270841v1_alt', 'chrUn_KI270744v1', 'chr18_KI270863v1_alt', 'chr18_GL383569v1_alt', 'chr12_GL877875v1_alt', 'chr21_KI270874v1_alt', 'chr3_KI270924v1_alt', 'chr1_KI270761v1_alt', 'chr3_KI270937v1_alt', 'chr22_KI270734v1_random', 'chr18_GL383570v1_alt', 'chr5_KI270794v1_alt', 'chr4_GL383527v1_alt', 'chrUn_GL000213v1', 'chr3_KI270936v1_alt', 'chr3_KI270934v1_alt', 'chr9_GL383539v1_alt', 'chr3_KI270895v1_alt', 'chr22_GL383582v2_alt', 'chr3_KI270782v1_alt', 'chr1_KI270892v1_alt', 'chrUn_GL000220v1', 'chr2_KI270767v1_alt', 'chr2_KI270715v1_random', 'chr2_KI270893v1_alt', 'chrUn_GL000218v1', 'chr18_GL383572v1_alt', 'chr8_KI270817v1_alt', 'chr4_KI270788v1_alt', 'chrUn_KI270749v1', 'chr7_KI270806v1_alt', 'chr7_KI270804v1_alt', 'chr18_KI270911v1_alt', 'chrUn_KI270741v1', 'chr17_KI270910v1_alt', 'chr19_KI270884v1_alt', 'chr19_GL383574v1_alt', 'chr19_KI270888v1_alt', 'chr3_GL000221v1_random', 'chr11_GL383547v1_alt', 'chr2_KI270716v1_random', 'chr12_GL383553v2_alt', 'chr6_KI270799v1_alt', 'chr22_KI270731v1_random', 'chrUn_KI270751v1', 'chrUn_KI270750v1', 'chr8_KI270818v1_alt', 'chrX_KI270881v1_alt', 'chr21_KI270873v1_alt', 'chr2_GL383521v1_alt', 'chr8_KI270814v1_alt', 'chr12_GL383552v1_alt', 'chrUn_KI270519v1', 'chr2_KI270775v1_alt', 'chr17_KI270907v1_alt', 'chrUn_GL000214v1', 'chr8_KI270901v1_alt', 'chr2_KI270770v1_alt', 'chr16_KI270854v1_alt', 'chr8_KI270819v1_alt', 'chr17_GL383564v2_alt', 'chr2_KI270772v1_alt', 'chr8_KI270815v1_alt', 'chr5_KI270795v1_alt', 'chr5_KI270898v1_alt', 'chr20_GL383577v2_alt', 'chr1_KI270708v1_random', 'chr7_KI270807v1_alt', 'chr5_KI270793v1_alt', 'chr6_GL383533v1_alt', 'chr2_GL383522v1_alt', 'chr19_KI270918v1_alt', 'chr12_GL383549v1_alt', 'chr2_KI270769v1_alt', 'chr4_KI270785v1_alt', 'chr12_KI270834v1_alt', 'chr7_GL383534v2_alt', 'chr20_KI270869v1_alt', 'chr21_GL383581v2_alt', 'chr3_KI270781v1_alt', 'chr17_KI270730v1_random', 'chrUn_KI270438v1', 'chr4_KI270787v1_alt', 'chr18_KI270864v1_alt', 'chr2_KI270771v1_alt', 'chr1_GL383519v1_alt', 'chr2_KI270768v1_alt', 'chr1_KI270760v1_alt', 'chr3_KI270783v1_alt', 'chr17_KI270859v1_alt', 'chr11_KI270902v1_alt', 'chr18_GL383568v1_alt', 'chr22_KI270737v1_random', 'chr13_KI270843v1_alt', 'chr22_KI270877v1_alt', 'chr5_GL383530v1_alt', 'chr11_KI270721v1_random', 'chr22_KI270738v1_random', 'chr22_GL383583v2_alt', 'chr2_GL582966v2_alt', 'chrUn_KI270748v1', 'chrUn_KI270435v1', 'chr5_GL000208v1_random', 'chrUn_KI270538v1', 'chr17_GL383566v1_alt', 'chr16_GL383557v1_alt', 'chr17_JH159148v1_alt', 'chr5_GL383532v1_alt', 'chr21_KI270872v1_alt', 'chrUn_KI270756v1', 'chr6_KI270758v1_alt', 'chr12_KI270833v1_alt', 'chr6_KI270802v1_alt', 'chr21_GL383580v2_alt', 'chr22_KB663609v1_alt', 'chr22_KI270739v1_random', 'chr9_GL383540v1_alt', 'chrUn_KI270757v1', 'chr2_KI270773v1_alt', 'chr17_JH159147v1_alt', 'chr11_KI270827v1_alt', 'chr1_KI270709v1_random', 'chrUn_KI270746v1', 'chr16_KI270856v1_alt', 'chr21_GL383578v2_alt', 'chrUn_KI270753v1', 'chr19_KI270868v1_alt', 'chr9_GL383542v1_alt', 'chr20_KI270871v1_alt', 'chr12_KI270836v1_alt', 'chr19_KI270865v1_alt', 'chr1_KI270764v1_alt', 'chrUn_KI270589v1', 'chr14_KI270726v1_random', 'chr19_KI270866v1_alt', 'chr22_KI270735v1_random', 'chr1_KI270711v1_random', 'chrUn_KI270745v1', 'chr1_KI270714v1_random', 'chr22_KI270732v1_random', 'chr1_KI270713v1_random', 'chrUn_KI270754v1', 'chr1_KI270710v1_random', 'chr12_KI270837v1_alt', 'chr9_KI270717v1_random', 'chr14_KI270724v1_random', 'chr9_KI270720v1_random', 'chr14_KI270723v1_random', 'chr9_KI270718v1_random', 'chrUn_KI270317v1', 'chr13_KI270842v1_alt', 'chrY_KI270740v1_random', 'chrUn_KI270755v1', 'chr8_KI270820v1_alt', 'chr1_KI270707v1_random', 'chrUn_KI270579v1', 'chrUn_KI270752v1', 'chrUn_KI270512v1', 'chrUn_KI270322v1', 'chrUn_GL000226v1', 'chrUn_KI270311v1', 'chrUn_KI270366v1', 'chrUn_KI270511v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_KI270581v1', 'chrUn_KI270582v1', 'chrUn_KI270515v1', 'chrUn_KI270588v1', 'chrUn_KI270591v1', 'chrUn_KI270522v1', 'chrUn_KI270507v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270320v1', 'chrUn_KI270382v1', 'chrUn_KI270468v1', 'chrUn_KI270467v1', 'chrUn_KI270362v1', 'chrUn_KI270517v1', 'chrUn_KI270593v1', 'chrUn_KI270528v1', 'chrUn_KI270587v1', 'chrUn_KI270364v1', 'chrUn_KI270371v1', 'chrUn_KI270333v1', 'chrUn_KI270374v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270510v1', 'chrUn_KI270390v1', 'chrUn_KI270375v1', 'chrUn_KI270420v1', 'chrUn_KI270509v1', 'chrUn_KI270315v1', 'chrUn_KI270302v1', 'chrUn_KI270518v1', 'chrUn_KI270530v1', 'chrUn_KI270304v1', 'chrUn_KI270418v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270508v1', 'chrUn_KI270303v1', 'chrUn_KI270381v1', 'chrUn_KI270529v1', 'chrUn_KI270425v1', 'chrUn_KI270396v1', 'chrUn_KI270363v1', 'chrUn_KI270386v1', 'chrUn_KI270465v1', 'chrUn_KI270383v1', 'chrUn_KI270384v1', 'chrUn_KI270330v1', 'chrUn_KI270372v1', 'chrUn_KI270548v1', 'chrUn_KI270580v1', 'chrUn_KI270387v1', 'chrUn_KI270391v1', 'chrUn_KI270305v1', 'chrUn_KI270373v1', 'chrUn_KI270422v1', 'chrUn_KI270316v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270583v1', 'chrUn_KI270334v1', 'chrUn_KI270429v1', 'chrUn_KI270393v1', 'chrUn_KI270516v1', 'chrUn_KI270389v1', 'chrUn_KI270466v1', 'chrUn_KI270388v1', 'chrUn_KI270544v1', 'chrUn_KI270310v1', 'chrUn_KI270412v1', 'chrUn_KI270395v1', 'chrUn_KI270376v1', 'chrUn_KI270337v1', 'chrUn_KI270335v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270329v1', 'chrUn_KI270419v1', 'chrUn_KI270336v1', 'chrUn_KI270312v1', 'chrUn_KI270539v1', 'chrUn_KI270385v1', 'chrUn_KI270423v1', 'chrUn_KI270392v1', 'chrUn_KI270394v1']
assembly size (max-length) 3209286105
max-width 4294967296
max_zoom: 22
chunk-size: 16777216
chrom-order [b'chr1' b'chr2' b'chr3' b'chr4' b'chr5' b'chr6' b'chr7' b'chr8' b'chr9'
b'chr10' b'chr11' b'chr12' b'chr13' b'chr14' b'chr15' b'chr16' b'chr17'
b'chr18' b'chr19' b'chr20' b'chr21' b'chr22' b'chrX' b'chrY' b'chrM'
b'chr15_KI270905v1_alt' b'chr6_GL000256v2_alt' b'chr6_GL000254v2_alt'
b'chr6_GL000251v2_alt' b'chr6_GL000253v2_alt' b'chr6_GL000250v2_alt'
b'chr6_GL000255v2_alt' b'chr6_GL000252v2_alt' b'chr17_KI270857v1_alt'
b'chr16_KI270853v1_alt' b'chr16_KI270728v1_random' b'chr17_GL000258v2_alt'
b'chr5_GL339449v2_alt' b'chr14_KI270847v1_alt' b'chr17_KI270908v1_alt'
b'chr14_KI270846v1_alt' b'chr5_KI270897v1_alt' b'chr7_KI270803v1_alt'
b'chr19_GL949749v2_alt' b'chr19_KI270938v1_alt' b'chr19_GL949750v2_alt'
b'chr19_GL949748v2_alt' b'chr19_GL949751v2_alt' b'chr19_GL949746v1_alt'
b'chr19_GL949752v1_alt' b'chr8_KI270821v1_alt' b'chr1_KI270763v1_alt'
b'chr6_KI270801v1_alt' b'chr19_GL949753v2_alt' b'chr19_GL949747v2_alt'
b'chr8_KI270822v1_alt' b'chr4_GL000257v2_alt' b'chr12_KI270904v1_alt'
b'chr4_KI270925v1_alt' b'chr15_KI270852v1_alt' b'chr15_KI270727v1_random'
b'chr9_KI270823v1_alt' b'chr15_KI270850v1_alt' b'chr1_KI270759v1_alt'
b'chr12_GL877876v1_alt' b'chrUn_KI270442v1' b'chr17_KI270862v1_alt'
b'chr15_GL383555v2_alt' b'chr19_GL383573v1_alt' b'chr4_KI270896v1_alt'
b'chr4_GL383528v1_alt' b'chr17_GL383563v3_alt' b'chr8_KI270810v1_alt'
b'chr1_GL383520v2_alt' b'chr1_KI270762v1_alt' b'chr15_KI270848v1_alt'
b'chr17_KI270909v1_alt' b'chr14_KI270844v1_alt' b'chr8_KI270900v1_alt'
b'chr10_GL383546v1_alt' b'chr13_KI270838v1_alt' b'chr8_KI270816v1_alt'
b'chr22_KI270879v1_alt' b'chr8_KI270813v1_alt' b'chr11_KI270831v1_alt'
b'chr15_GL383554v1_alt' b'chr8_KI270811v1_alt' b'chr18_GL383567v1_alt'
b'chrX_KI270880v1_alt' b'chr8_KI270812v1_alt' b'chr19_KI270921v1_alt'
b'chr17_KI270729v1_random' b'chr17_JH159146v1_alt' b'chrX_KI270913v1_alt'
b'chr6_KI270798v1_alt' b'chr7_KI270808v1_alt' b'chr22_KI270876v1_alt'
b'chr15_KI270851v1_alt' b'chr22_KI270875v1_alt' b'chr1_KI270766v1_alt'
b'chr19_KI270882v1_alt' b'chr3_KI270778v1_alt' b'chr15_KI270849v1_alt'
b'chr4_KI270786v1_alt' b'chr12_KI270835v1_alt' b'chr17_KI270858v1_alt'
b'chr19_KI270867v1_alt' b'chr16_KI270855v1_alt' b'chr8_KI270926v1_alt'
b'chr5_GL949742v1_alt' b'chr3_KI270780v1_alt' b'chr17_GL383565v1_alt'
b'chr2_KI270774v1_alt' b'chr4_KI270790v1_alt' b'chr11_KI270927v1_alt'
b'chr19_KI270932v1_alt' b'chr11_KI270903v1_alt' b'chr2_KI270894v1_alt'
b'chr14_GL000225v1_random' b'chrUn_KI270743v1' b'chr11_KI270832v1_alt'
b'chr7_KI270805v1_alt' b'chr4_GL000008v2_random' b'chr7_KI270809v1_alt'
b'chr19_KI270887v1_alt' b'chr4_KI270789v1_alt' b'chr3_KI270779v1_alt'
b'chr19_KI270914v1_alt' b'chr19_KI270886v1_alt' b'chr11_KI270829v1_alt'
b'chr14_GL000009v2_random' b'chr21_GL383579v2_alt' b'chr11_JH159136v1_alt'
b'chr19_KI270930v1_alt' b'chrUn_KI270747v1' b'chr18_GL383571v1_alt'
b'chr19_KI270920v1_alt' b'chr6_KI270797v1_alt' b'chr3_KI270935v1_alt'
b'chr17_KI270861v1_alt' b'chr15_KI270906v1_alt' b'chr5_KI270791v1_alt'
b'chr14_KI270722v1_random' b'chr16_GL383556v1_alt' b'chr13_KI270840v1_alt'
b'chr14_GL000194v1_random' b'chr11_JH159137v1_alt' b'chr19_KI270917v1_alt'
b'chr7_KI270899v1_alt' b'chr19_KI270923v1_alt' b'chr10_KI270825v1_alt'
b'chr19_GL383576v1_alt' b'chr19_KI270922v1_alt' b'chrUn_KI270742v1'
b'chr22_KI270878v1_alt' b'chr19_KI270929v1_alt' b'chr11_KI270826v1_alt'
b'chr6_KB021644v2_alt' b'chr17_GL000205v2_random' b'chr1_KI270765v1_alt'
b'chr19_KI270916v1_alt' b'chr19_KI270890v1_alt' b'chr3_KI270784v1_alt'
b'chr12_GL383551v1_alt' b'chr20_KI270870v1_alt' b'chrUn_GL000195v1'
b'chr1_GL383518v1_alt' b'chr22_KI270736v1_random' b'chr10_KI270824v1_alt'
b'chr14_KI270845v1_alt' b'chr3_GL383526v1_alt' b'chr13_KI270839v1_alt'
b'chr22_KI270733v1_random' b'chrUn_GL000224v1' b'chr10_GL383545v1_alt'
b'chrUn_GL000219v1' b'chr5_KI270792v1_alt' b'chr17_KI270860v1_alt'
b'chr19_GL000209v2_alt' b'chr11_KI270830v1_alt' b'chr9_KI270719v1_random'
b'chrUn_GL000216v2' b'chr22_KI270928v1_alt' b'chr1_KI270712v1_random'
b'chr6_KI270800v1_alt' b'chr1_KI270706v1_random' b'chr2_KI270776v1_alt'
b'chr18_KI270912v1_alt' b'chr3_KI270777v1_alt' b'chr5_GL383531v1_alt'
b'chr3_JH636055v2_alt' b'chr14_KI270725v1_random' b'chr5_KI270796v1_alt'
b'chr9_GL383541v1_alt' b'chr19_KI270885v1_alt' b'chr19_KI270919v1_alt'
b'chr19_KI270889v1_alt' b'chr19_KI270891v1_alt' b'chr19_KI270915v1_alt'
b'chr19_KI270933v1_alt' b'chr19_KI270883v1_alt' b'chr19_GL383575v2_alt'
b'chr19_KI270931v1_alt' b'chr12_GL383550v2_alt' b'chr13_KI270841v1_alt'
b'chrUn_KI270744v1' b'chr18_KI270863v1_alt' b'chr18_GL383569v1_alt'
b'chr12_GL877875v1_alt' b'chr21_KI270874v1_alt' b'chr3_KI270924v1_alt'
b'chr1_KI270761v1_alt' b'chr3_KI270937v1_alt' b'chr22_KI270734v1_random'
b'chr18_GL383570v1_alt' b'chr5_KI270794v1_alt' b'chr4_GL383527v1_alt'
b'chrUn_GL000213v1' b'chr3_KI270936v1_alt' b'chr3_KI270934v1_alt'
b'chr9_GL383539v1_alt' b'chr3_KI270895v1_alt' b'chr22_GL383582v2_alt'
b'chr3_KI270782v1_alt' b'chr1_KI270892v1_alt' b'chrUn_GL000220v1'
b'chr2_KI270767v1_alt' b'chr2_KI270715v1_random' b'chr2_KI270893v1_alt'
b'chrUn_GL000218v1' b'chr18_GL383572v1_alt' b'chr8_KI270817v1_alt'
b'chr4_KI270788v1_alt' b'chrUn_KI270749v1' b'chr7_KI270806v1_alt'
b'chr7_KI270804v1_alt' b'chr18_KI270911v1_alt' b'chrUn_KI270741v1'
b'chr17_KI270910v1_alt' b'chr19_KI270884v1_alt' b'chr19_GL383574v1_alt'
b'chr19_KI270888v1_alt' b'chr3_GL000221v1_random' b'chr11_GL383547v1_alt'
b'chr2_KI270716v1_random' b'chr12_GL383553v2_alt' b'chr6_KI270799v1_alt'
b'chr22_KI270731v1_random' b'chrUn_KI270751v1' b'chrUn_KI270750v1'
b'chr8_KI270818v1_alt' b'chrX_KI270881v1_alt' b'chr21_KI270873v1_alt'
b'chr2_GL383521v1_alt' b'chr8_KI270814v1_alt' b'chr12_GL383552v1_alt'
b'chrUn_KI270519v1' b'chr2_KI270775v1_alt' b'chr17_KI270907v1_alt'
b'chrUn_GL000214v1' b'chr8_KI270901v1_alt' b'chr2_KI270770v1_alt'
b'chr16_KI270854v1_alt' b'chr8_KI270819v1_alt' b'chr17_GL383564v2_alt'
b'chr2_KI270772v1_alt' b'chr8_KI270815v1_alt' b'chr5_KI270795v1_alt'
b'chr5_KI270898v1_alt' b'chr20_GL383577v2_alt' b'chr1_KI270708v1_random'
b'chr7_KI270807v1_alt' b'chr5_KI270793v1_alt' b'chr6_GL383533v1_alt'
b'chr2_GL383522v1_alt' b'chr19_KI270918v1_alt' b'chr12_GL383549v1_alt'
b'chr2_KI270769v1_alt' b'chr4_KI270785v1_alt' b'chr12_KI270834v1_alt'
b'chr7_GL383534v2_alt' b'chr20_KI270869v1_alt' b'chr21_GL383581v2_alt'
b'chr3_KI270781v1_alt' b'chr17_KI270730v1_random' b'chrUn_KI270438v1'
b'chr4_KI270787v1_alt' b'chr18_KI270864v1_alt' b'chr2_KI270771v1_alt'
b'chr1_GL383519v1_alt' b'chr2_KI270768v1_alt' b'chr1_KI270760v1_alt'
b'chr3_KI270783v1_alt' b'chr17_KI270859v1_alt' b'chr11_KI270902v1_alt'
b'chr18_GL383568v1_alt' b'chr22_KI270737v1_random' b'chr13_KI270843v1_alt'
b'chr22_KI270877v1_alt' b'chr5_GL383530v1_alt' b'chr11_KI270721v1_random'
b'chr22_KI270738v1_random' b'chr22_GL383583v2_alt' b'chr2_GL582966v2_alt'
b'chrUn_KI270748v1' b'chrUn_KI270435v1' b'chr5_GL000208v1_random'
b'chrUn_KI270538v1' b'chr17_GL383566v1_alt' b'chr16_GL383557v1_alt'
b'chr17_JH159148v1_alt' b'chr5_GL383532v1_alt' b'chr21_KI270872v1_alt'
b'chrUn_KI270756v1' b'chr6_KI270758v1_alt' b'chr12_KI270833v1_alt'
b'chr6_KI270802v1_alt' b'chr21_GL383580v2_alt' b'chr22_KB663609v1_alt'
b'chr22_KI270739v1_random' b'chr9_GL383540v1_alt' b'chrUn_KI270757v1'
b'chr2_KI270773v1_alt' b'chr17_JH159147v1_alt' b'chr11_KI270827v1_alt'
b'chr1_KI270709v1_random' b'chrUn_KI270746v1' b'chr16_KI270856v1_alt'
b'chr21_GL383578v2_alt' b'chrUn_KI270753v1' b'chr19_KI270868v1_alt'
b'chr9_GL383542v1_alt' b'chr20_KI270871v1_alt' b'chr12_KI270836v1_alt'
b'chr19_KI270865v1_alt' b'chr1_KI270764v1_alt' b'chrUn_KI270589v1'
b'chr14_KI270726v1_random' b'chr19_KI270866v1_alt'
b'chr22_KI270735v1_random' b'chr1_KI270711v1_random' b'chrUn_KI270745v1'
b'chr1_KI270714v1_random' b'chr22_KI270732v1_random'
b'chr1_KI270713v1_random' b'chrUn_KI270754v1' b'chr1_KI270710v1_random'
b'chr12_KI270837v1_alt' b'chr9_KI270717v1_random'
b'chr14_KI270724v1_random' b'chr9_KI270720v1_random'
b'chr14_KI270723v1_random' b'chr9_KI270718v1_random' b'chrUn_KI270317v1'
b'chr13_KI270842v1_alt' b'chrY_KI270740v1_random' b'chrUn_KI270755v1'
b'chr8_KI270820v1_alt' b'chr1_KI270707v1_random' b'chrUn_KI270579v1'
b'chrUn_KI270752v1' b'chrUn_KI270512v1' b'chrUn_KI270322v1'
b'chrUn_GL000226v1' b'chrUn_KI270311v1' b'chrUn_KI270366v1'
b'chrUn_KI270511v1' b'chrUn_KI270448v1' b'chrUn_KI270521v1'
b'chrUn_KI270581v1' b'chrUn_KI270582v1' b'chrUn_KI270515v1'
b'chrUn_KI270588v1' b'chrUn_KI270591v1' b'chrUn_KI270522v1'
b'chrUn_KI270507v1' b'chrUn_KI270590v1' b'chrUn_KI270584v1'
b'chrUn_KI270320v1' b'chrUn_KI270382v1' b'chrUn_KI270468v1'
b'chrUn_KI270467v1' b'chrUn_KI270362v1' b'chrUn_KI270517v1'
b'chrUn_KI270593v1' b'chrUn_KI270528v1' b'chrUn_KI270587v1'
b'chrUn_KI270364v1' b'chrUn_KI270371v1' b'chrUn_KI270333v1'
b'chrUn_KI270374v1' b'chrUn_KI270411v1' b'chrUn_KI270414v1'
b'chrUn_KI270510v1' b'chrUn_KI270390v1' b'chrUn_KI270375v1'
b'chrUn_KI270420v1' b'chrUn_KI270509v1' b'chrUn_KI270315v1'
b'chrUn_KI270302v1' b'chrUn_KI270518v1' b'chrUn_KI270530v1'
b'chrUn_KI270304v1' b'chrUn_KI270418v1' b'chrUn_KI270424v1'
b'chrUn_KI270417v1' b'chrUn_KI270508v1' b'chrUn_KI270303v1'
b'chrUn_KI270381v1' b'chrUn_KI270529v1' b'chrUn_KI270425v1'
b'chrUn_KI270396v1' b'chrUn_KI270363v1' b'chrUn_KI270386v1'
b'chrUn_KI270465v1' b'chrUn_KI270383v1' b'chrUn_KI270384v1'
b'chrUn_KI270330v1' b'chrUn_KI270372v1' b'chrUn_KI270548v1'
b'chrUn_KI270580v1' b'chrUn_KI270387v1' b'chrUn_KI270391v1'
b'chrUn_KI270305v1' b'chrUn_KI270373v1' b'chrUn_KI270422v1'
b'chrUn_KI270316v1' b'chrUn_KI270338v1' b'chrUn_KI270340v1'
b'chrUn_KI270583v1' b'chrUn_KI270334v1' b'chrUn_KI270429v1'
b'chrUn_KI270393v1' b'chrUn_KI270516v1' b'chrUn_KI270389v1'
b'chrUn_KI270466v1' b'chrUn_KI270388v1' b'chrUn_KI270544v1'
b'chrUn_KI270310v1' b'chrUn_KI270412v1' b'chrUn_KI270395v1'
b'chrUn_KI270376v1' b'chrUn_KI270337v1' b'chrUn_KI270335v1'
b'chrUn_KI270378v1' b'chrUn_KI270379v1' b'chrUn_KI270329v1'
b'chrUn_KI270419v1' b'chrUn_KI270336v1' b'chrUn_KI270312v1'
b'chrUn_KI270539v1' b'chrUn_KI270385v1' b'chrUn_KI270423v1'
b'chrUn_KI270392v1' b'chrUn_KI270394v1']
chrom: chr1
Killed
For this test, I am using v0.3.11 of the pyBigWig library, which appears to be the current version.
I am wondering if there are perhaps specific versions of Python or libraries I should be using for data conversion, or are there memory requirements for conversion that would be satisfied with a host with more memory?
alexpreynolds commented
Running the same conversion on a t2.large EC2 instance running Ubuntu Xenial v16.04 seemed to work without errors.