Primer Design Module Error

[udube]

Hello,

I receive the following error when attempting to run the Primer Design module:

Command:

circtools primex -d /DCC/CircCoordinates -g gencode.v26.primary_assembly.annotation.gtf -f GRCh38.primary_assembly.genome.fa -O hs -G CIRC123 -T "CIRC123"

Error:

Sending 40 primers to BLAST This may take a few minutes, please be patient. Error in colnames<-(*tmp*, value = c("Annotation", "Chr", "Start", : length of 'dimnames' [2] not equal to array extent Calls: %>% ... _fseq -> freduce -> -> kable -> colnames<- Execution halted Writing results to ./CIRC123.html

I am using a CircCoordinates file generated using DCC.

Thanks

[tjakobi]

Dear @udube,

thank you for your feedback. Could please look for the following files:

/tmp/circtools_flanking_exons.tmp /tmp/circtools_blast_results.tmp (/tmp/circtools_blast_results.xml)

and attach them here? The first two are probably already enough.

Thank you, Tobias

[udube]

Dear @tjakobi,

Thank you for your prompt response. I have attached the files you requested (circtools_blast_results.zip). I am also including the program output.

Start parsing GTF file
Start merging GTF file
***** WARNING: File /tmp/pybedtools.d3s8c_mq.tmp has inconsistent naming convention for record:
GL000009.2      56140   58376   name    0       -

***** WARNING: File /tmp/pybedtools.d3s8c_mq.tmp has inconsistent naming convention for record:
GL000009.2      56140   58376   name    0       -

extracting flanking exons for circRNA # 1 CASC4_chr15_44322965_44338317_+
***** WARNING: File /tmp/pybedtools.d3s8c_mq.tmp has inconsistent naming convention for record:
GL000009.2      56140   58376   name    0       -

***** WARNING: File /tmp/pybedtools.d3s8c_mq.tmp has inconsistent naming convention for record:
GL000009.2      56140   58376   name    0       -

extracting flanking exons for circRNA # 2 CASC4_chr15_44328685_44338317_+
***** WARNING: File /tmp/pybedtools.d3s8c_mq.tmp has inconsistent naming convention for record:
GL000009.2      56140   58376   name    0       -

***** WARNING: File /tmp/pybedtools.d3s8c_mq.tmp has inconsistent naming convention for record:
GL000009.2      56140   58376   name    0       -

Could not identify the exact exon-border of the circRNA.
Will continue with non-annotated, manually extracted sequence.
extracting flanking exons for circRNA # 3 CASC4_chr15_44331940_44338317_+
***** WARNING: File /tmp/pybedtools.d3s8c_mq.tmp has inconsistent naming convention for record:
GL000009.2      56140   58376   name    0       -

***** WARNING: File /tmp/pybedtools.d3s8c_mq.tmp has inconsistent naming convention for record:
GL000009.2      56140   58376   name    0       -

extracting flanking exons for circRNA # 4 CASC4_chr15_44331988_44338317_+
***** WARNING: File /tmp/pybedtools.d3s8c_mq.tmp has inconsistent naming convention for record:
GL000009.2      56140   58376   name    0       -

***** WARNING: File /tmp/pybedtools.d3s8c_mq.tmp has inconsistent naming convention for record:
GL000009.2      56140   58376   name    0       -

extracting flanking exons for circRNA # 5 CASC4_chr15_44337763_44338317_+
***** WARNING: File /tmp/pybedtools.d3s8c_mq.tmp has inconsistent naming convention for record:
GL000009.2      56140   58376   name    0       -

***** WARNING: File /tmp/pybedtools.d3s8c_mq.tmp has inconsistent naming convention for record:
GL000009.2      56140   58376   name    0       -

extracting flanking exons for circRNA # 6 CASC4_chr15_44379690_44380976_+
Sending 33 primers to BLAST
This may take a few minutes, please be patient.
Error in `colnames<-`(`*tmp*`, value = c("Annotation", "Chr", "Start",  :
  length of 'dimnames' [2] not equal to array extent
Calls: %>% ... _fseq -> freduce -> <Anonymous> -> kable -> colnames<-
Execution halted
Writing results to ./CASC4.html

Please note that even if I use a GTF file without the unplaced contigs I still receive the error but do not receive the warnings.

[tjakobi]

I just remembered #70 , that seems highly related. However, since there was no new release the fix is not yet on pypi.org. Could you please clone the current master branch of the repository and update your circtools installation? I'd assume that should fix your error.

[udube]

Thank you. Following the instructions you provided has solved this issue. I appreciate your prompt responses and help.