Thanks for supporting this R package. I installed fragCounter from github on Feb 4, 2022. Using that version, I ran the suggested test using the bundled test files:
Are there any troubleshooting or solution options to resolve this error?
/usr/local/lib/R/library/fragCounter/extdata# ./frag -b chr21.bam -d gcMAP21/ -w 200
<snip>
Calling samtools view -f 0x02 -F 0x10 chr21.bam -q 1 | cut -f "3,4,9"
Starting fragment count on chr21.bam with bin size 200 and min mapQ 1 and insert size limit 10000 with midpoint set to TRUE
Finished computing coverage, and making GRanges
Finished acquiring coverage
Loaded GC and mappability
length cov is 15509063, length gc is 240650, length map is 240650
Synced coverage, GC, and mappability
Modified gc / mappability correction
Converting to data.table
Grouping intervals
Defining 500 fold collapsed ranges
Presegmenting at 100000 bp scale
Aggregating coverage within levels
Mono scale correction
Correcting coverage at individual scales
Correcting coverage at 200 bp scale, with 234722 intervals
Quantile filtering response and covariates
Response min quantile: 0 max quantile: 0
Nominated 0 of 234722 data points for loess fitting
Converting to GRanges
Made GRanges
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'con' in selecting a method for function 'export': invalid class "BigWigFile" object: undefined class for slot "resource" ("characterORconnection")
Calls: fragCounter ... <Anonymous> -> new -> initialize -> initialize -> validObject
In addition: Warning messages:
1: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'bamUtils'
2: replacing previous import 'GenomicAlignments::second' by 'data.table::second' when loading 'bamUtils'
3: replacing previous import 'GenomicAlignments::last' by 'data.table::last' when loading 'bamUtils'
4: replacing previous import 'GenomicAlignments::first' by 'data.table::first' when loading 'bamUtils'
5: closing unused connection 3 (chr21.bam)
6: In value[[3L]](cond) : DNACopy error moving on without segmenting
7: In FUN(as.data.frame(grs[[i]]), fields, seg = seg) :
Not enough samples for loess fitting - check to see if missing or truncated data?
Execution halted
Thanks for supporting this R package. I installed
fragCounterfrom github on Feb 4, 2022. Using that version, I ran the suggested test using the bundled test files:/usr/local/lib/R/library/fragCounter/extdata# ./frag -b chr21.bam -d gcMAP21/ -w 200The run failed with the trace pasted below.
Are there any troubleshooting or solution options to resolve this error?