hello @bjtrost please i am new to some of these softwares, i tried calling CNV with some set of data i have following the ERDS pipeline but it keeps on with these errors, please could you let me know what the problem is?
these are my inputs :
perl erds_pipeline.pl -b /mnt/e/SNV_GATK_NVG/pass_snv/Quartet_DNA_ILM_NVG_LCL5_1_20170329_sorted_RG_RmDup.bam -v /mnt/e/SNV_GATK_NVG/Quartet_DNA_ILM_NVG_LCL5_1_20170329_XJT_BWA_HC_SNV_RAW.vcf -o /mnt/e/SNV_GATK_NVG/benue/ -r /mnt/e/ERDS/erds_tcag/src/GRCh38_full_analysis_set_plus_decoy_hla.fa
and i get errors like this:
Error code for chrHLA-DRB1*16:02:01 is 0
[Tue Dec 11 17:49:18 2018] PID 9215 is performing computation for chrchrUn_JTFH01001990v1_decoy
Error code for chrchrUn_JTFH01001993v1_decoy is 0
Error: File /mnt/e/SNV_GATK_NVG/benue//cnv/gcbin/0.gcbin not found
Use of uninitialized value $in in substitution (s///) at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 62.
Use of uninitialized value $in in split at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 63.
Use of uninitialized value in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 64.
Use of uninitialized value in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 64.
Error: File /mnt/e/SNV_GATK_NVG/benue//cnv/gcbin/1.gcbin not found
Use of uninitialized value $in in substitution (s///) at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 62.
Use of uninitialized value $in in split at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 63.
Use of uninitialized value in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 64.
Use of uninitialized value in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 64.
Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166.
Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166.
Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166.
Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166.
Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166.
Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166.
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr1.rd
Can't open /mnt/e/SNV_GATK_NVG/benue//cnv/chr1.vit at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 95.
17:51:48 Dec 11 2018 ERDS finished step 2 in RPG...
17:51:48 Dec 11 2018 ERDS stared step 3 in RPG...
[Tue Dec 11 17:51:48 2018] PID 17085 is performing computation for chrchrY
[Tue Dec 11 17:51:48 2018] PID 17086 is performing computation for chrchrX
[Tue Dec 11 17:51:48 2018] PID 17088 is performing computation for chrchr22
[Tue Dec 11 17:51:48 2018] PID 17090 is performing computation for chrchr21
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chrX.rd
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr22.rd
[Tue Dec 11 17:51:48 2018] PID 17086 is performing computation for chrchr19
[Tue Dec 11 17:51:48 2018] PID 17085 is performing computation for chrchr20
[Tue Dec 11 17:51:48 2018] PID 17088 is performing computation for chrchr18
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr21.rd
[Tue Dec 11 17:51:48 2018] PID 17090 is performing computation for chrchr17
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr19.rd
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr20.rd
no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr17.rd
i couldn't paste all the errors, so i picked where they all differs. please can you help how i could fix this? thank you
hello @bjtrost please i am new to some of these softwares, i tried calling CNV with some set of data i have following the ERDS pipeline but it keeps on with these errors, please could you let me know what the problem is? these are my inputs : perl erds_pipeline.pl -b /mnt/e/SNV_GATK_NVG/pass_snv/Quartet_DNA_ILM_NVG_LCL5_1_20170329_sorted_RG_RmDup.bam -v /mnt/e/SNV_GATK_NVG/Quartet_DNA_ILM_NVG_LCL5_1_20170329_XJT_BWA_HC_SNV_RAW.vcf -o /mnt/e/SNV_GATK_NVG/benue/ -r /mnt/e/ERDS/erds_tcag/src/GRCh38_full_analysis_set_plus_decoy_hla.fa
and i get errors like this:
Error code for chrHLA-DRB1*16:02:01 is 0 [Tue Dec 11 17:49:18 2018] PID 9215 is performing computation for chrchrUn_JTFH01001990v1_decoy Error code for chrchrUn_JTFH01001993v1_decoy is 0 Error: File /mnt/e/SNV_GATK_NVG/benue//cnv/gcbin/0.gcbin not found Use of uninitialized value $in in substitution (s///) at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 62. Use of uninitialized value $in in split at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 63. Use of uninitialized value in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 64. Use of uninitialized value in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 64. Error: File /mnt/e/SNV_GATK_NVG/benue//cnv/gcbin/1.gcbin not found Use of uninitialized value $in in substitution (s///) at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 62. Use of uninitialized value $in in split at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 63. Use of uninitialized value in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 64. Use of uninitialized value in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 64. Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166. Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166. Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166. Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166. Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166. Redundant argument in printf at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 166. no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr1.rd Can't open /mnt/e/SNV_GATK_NVG/benue//cnv/chr1.vit at /mnt/e/SNV_GATK_NVG/benue//script/em.pl line 95. 17:51:48 Dec 11 2018 ERDS finished step 2 in RPG... 17:51:48 Dec 11 2018 ERDS stared step 3 in RPG... [Tue Dec 11 17:51:48 2018] PID 17085 is performing computation for chrchrY [Tue Dec 11 17:51:48 2018] PID 17086 is performing computation for chrchrX [Tue Dec 11 17:51:48 2018] PID 17088 is performing computation for chrchr22 [Tue Dec 11 17:51:48 2018] PID 17090 is performing computation for chrchr21 no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chrX.rd no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr22.rd [Tue Dec 11 17:51:48 2018] PID 17086 is performing computation for chrchr19 [Tue Dec 11 17:51:48 2018] PID 17085 is performing computation for chrchr20 [Tue Dec 11 17:51:48 2018] PID 17088 is performing computation for chrchr18 no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr21.rd [Tue Dec 11 17:51:48 2018] PID 17090 is performing computation for chrchr17 no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr19.rd no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr20.rd no chromosome /mnt/e/SNV_GATK_NVG/benue//cnv/chr17.rd
i couldn't paste all the errors, so i picked where they all differs. please can you help how i could fix this? thank you