Entering edit mode
3.4 years ago
pixie@bioinfo
★
1.5k
Hello, I am using Diffreps for differential ChIPseq analysis. I keep getting this error which I am unable to fix. The details of the input files and the result files are given below. Any insight is greatly appreciated.
ERROR: median function called for an empty array!
Command: diffReps.pl --treatment hd2b_K9ac.bed --control Col_K9ac.bed --pval 0.05 --mode peak --nsd sharp --meth gt --chrlen TAIR10.sizes.genome.bed --nproc 8 --report diff_rep_Col_K9ac_hd2b_K9ac
**head hd2b_K9ac.bed**
1 0 76 NB501040:259:HHGFMBGXF:2:12209:7824:3953 42 - 76M
1 29 105 NB501040:259:HHGFMBGXF:4:13612:20198:6923 42 + 76M
1 34 110 NB501040:259:HHGFMBGXF:2:21112:20170:13187 42 - 76M
1 36 112 NB501040:259:HHGFMBGXF:4:13610:11015:17275 42 + 76M
1 38 114 NB501040:259:HHGFMBGXF:2:23204:2334:13315 42 + 76M
1 45 121 NB501040:259:HHGFMBGXF:2:12305:24201:18773 42 + 76M
1 48 124 NB501040:259:HHGFMBGXF:2:12312:11041:17999 42 + 76M
1 64 140 NB501040:259:HHGFMBGXF:1:13307:14924:13435 42 + 76M
1 65 141 NB501040:259:HHGFMBGXF:3:23402:11064:11492 42 - 76M
1 71 147 NB501040:259:HHGFMBGXF:4:13610:14215:13849 42 - 76M
head Col_K9ac.bed
1 14 90 NB501040:259:HHGFMBGXF:2:22103:14998:7644 42 - 76M
1 21 97 NB501040:259:HHGFMBGXF:3:13409:2681:8971 42 + 76M
1 23 99 NB501040:259:HHGFMBGXF:2:11112:10561:11936 42 + 76M
1 40 116 NB501040:259:HHGFMBGXF:4:22407:3614:17196 42 + 76M
1 41 117 NB501040:259:HHGFMBGXF:1:13209:20086:16349 42 + 76M
1 63 139 NB501040:259:HHGFMBGXF:2:23204:14388:16745 42 - 76M
1 68 144 NB501040:259:HHGFMBGXF:2:12202:7185:10396 42 - 76M
1 69 145 NB501040:259:HHGFMBGXF:1:11307:21730:16698 42 + 76M
1 73 149 NB501040:259:HHGFMBGXF:4:11508:24118:6667 42 + 76M
1 87 163 NB501040:259:HHGFMBGXF:2:12203:7189:3711 42 - 76M
**Results file:**
# diffReps version: 1.55.3
## Parameter Settings ##
# Treatment files: hd2b.bed
# Control files: Col_K9ac.bed
# Treatment background: None Specified
# Control background: None Specified
# Output file: diff_rep_Col_K9ac_hd2b_K9ac
# Statistical Test: G-test
# Use robust estimation: yes
# Number of deviation cutoff: 20
# Alpha in right-trimmed mean: 0.05
# P-value cutoff: 0.05
# Window size: 1000
# Step size: 100
# Gap size: 0
# Fragment size: 100
# Number of processors used: 8
# Full command used: /opt/share/CPAN/Debian-Buster/ModuleCPAN/bin/diffReps.pl --treatment /K/CHROCYC/Deep-sequencing_Raw_Data/ChIPseq_Rim_hd2b_hda19/test-Rim/sorted_dedupPCR_aboveMAPQ30_trimmed_hd2b_K9ac_Rim_S9_R1_001_bowtie_res.bed --control /K/CHROCYC/Deep-sequencing_Raw_Data/ChIPseq_Rim_hd2b_hda19/test-Rim/sorted_dedupPCR_aboveMAPQ30_trimmed_Col_K9ac_Rim_S5_R1_001_bowtie_res.bed --pval 0.05 --mode peak --nsd sharp --meth gt --chrlen /K/CHROCYC/Rim/tools/TAIR10.sizes.genome_noChr.bed --nproc 8 --report diff_rep__Col_K9ac__hd2b_K9ac
# Split BED files done in 206 seconds.
