Hi everyone,
I have been using ABACAS in order to map contigs to a reference genome and all the contigs from mira, ray, newbler, cap3 seem to run and produce results except for CLCworkbench contigs file
I am getting this error:
# CONSTRUCTIONTIME /usr/bin/mummer nucmer.ntref 1.14
# reading input file "/home/parinita/Documents/CSC8398/Abacas_mapping/CLC_workbench.fasta" of length 2814092
# matching query-file "/home/parinita/Documents/CSC8398/Abacas_mapping/CLC_workbench.fasta"
# against subject-file "nucmer.ntref"
# COMPLETETIME /usr/bin/mummer nucmer.ntref 5.95
# SPACE /usr/bin/mummer nucmer.ntref 5.65
4: FINISHING DATA
ERROR: Could not parse input from 'Query File'.
Please check the filename and format, or file a bug report
ERROR: postnuc returned non-zero
Use of uninitialized value in addition (+) at abacas.1.3.1.pl line 1001.
Total contigs = 0
Use of uninitialized value $id in print at abacas.1.3.1.pl line 1013.
Use of uninitialized value $id in print at abacas.1.3.1.pl line 1014.
Use of uninitialized value $id in print at abacas.1.3.1.pl line 1015.
I am pretty sure, my file is in the correct format because I have used it with other software before.
So if anyone could please help me?
Thank you.
I have been using ABACAS in order to map contigs to a reference genome and all the contigs from mira, ray, newbler, cap3 seem to run and produce results except for CLCworkbench contigs file
I am getting this error:
# CONSTRUCTIONTIME /usr/bin/mummer nucmer.ntref 1.14
# reading input file "/home/parinita/Documents/CSC8398/Abacas_mapping/CLC_workbench.fasta" of length 2814092
# matching query-file "/home/parinita/Documents/CSC8398/Abacas_mapping/CLC_workbench.fasta"
# against subject-file "nucmer.ntref"
# COMPLETETIME /usr/bin/mummer nucmer.ntref 5.95
# SPACE /usr/bin/mummer nucmer.ntref 5.65
4: FINISHING DATA
ERROR: Could not parse input from 'Query File'.
Please check the filename and format, or file a bug report
ERROR: postnuc returned non-zero
Use of uninitialized value in addition (+) at abacas.1.3.1.pl line 1001.
Total contigs = 0
Use of uninitialized value $id in print at abacas.1.3.1.pl line 1013.
Use of uninitialized value $id in print at abacas.1.3.1.pl line 1014.
Use of uninitialized value $id in print at abacas.1.3.1.pl line 1015.
I am pretty sure, my file is in the correct format because I have used it with other software before.
So if anyone could please help me?
Thank you.
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