swan_scan halted

[Derek Van Booven]

Hi,

I've run into a problem in swan_scan. The swan_stat works perfectly, but the scan stage halts.

Here is my command line :

$SWAN_BIN/swan_scan -c 21 /reference/human_g1k_v37.fasta -n /reference/test/gap.bed 39.21.recal.bam

Here is the relevant return :

-Info: swan_scan vesion: 0.3.0 -Info: invoking command: /share/opt/R/3.3.1/lib64/R/bin/exec/R --slave --no-restore --file=/mihg/users/dvanbooven/R/x86_64-pc-linux-gnu-library/3.3/swan/swan_scan --args -c 21 /reference/human_g1k_v37.fasta -n /reference/test/gap.bed 39.21.recal.bam all chrs: 21 -Info: doing scan, gtk=68.176s,gmk=(rss,vsz) 3212400 3526760kb -Info: apply_chr: 21 , rg_files: 1 [1] "39.21.recal.bam"

-Info: apply_chr: 21 , sp_prefix: [1] "39.21.recal.21" -Info: apply_chr: 21 , rg_prefix: 1 [1] "39.21.recal.21.rg1"

=Info apply_scan: group 1 of 1 groups within sample 1 of 1 samples =Info apply_scan: rg_file 39.21.recal.bam =Info apply_scan: rg_prefix 39.21.recal.21.rg1 =Info apply_scan: rg_out 39.21.recal.21.rg1 =Info: find rg isize modes at 419 with densities 0.003414029 ==Info: scan_bam: t_start= 1 t_end= 1000000 ; 1 -th of 49 Error: 'as.vector' is not an exported object from 'namespace:IRanges' Execution halted

Any help is much appreciated, Derek

[Ross Murphy]

Also have the same issue and swan_stat works fine.

Command line:

R/x86/3.4/swan/swan_scan -c a /mnt/scratch/users/40057929/BWA/Homo_sapiens/NCBI/GRCh38Decoy/Sequence/BWAIndex/genome.fa /mnt/scratch/users/40057929/MCLHighNov2016/Batch1/04-0309/04-0309-01_S2.bam

Error code:

==Info: scan_bam: t_start= 1 t_end= 1000000 ; 1 -th of 249 Error: 'as.vector' is not an exported object from 'namespace:IRanges' Execution halted

Did you find a relevant fix Derek? Or any other help?

[Sameera]

We are also facing the same issue. Is there any update in resolving the issue.

/R/x86_64-pc-linux-gnu-library/3.4/swan$ ./swan_scan -c chr9 -v 850000000 -a reference_gen/ref.fa test.sorted.markdup.bam

==Info: scan_bam: t_start= 1 t_end= 1000000 ; 1 -th of 73 Error: 'as.vector' is not an exported object from 'namespace:IRanges' Execution halted

[Ross Murphy]

I contacted the author via e-mail last week and no reply of yet, will post any resolutions to the problem if found.

[Charlie Xia]

Apologize for the late reply. I have recently updated the package which should resolved the above issue.