Demo sample works but when I use my own sample and the reference used during the alignment (bwa mem) I run it the error below. Mapped reads contain the necessary MC and MQ tags and the sequence names are the same in the reference fasta, bam header, and the contig_map file generated by Insurveyor. I've tried different reference files, filtering to only reads with MC and MQ tags, using only mapped reads, etc. but I run into the same error. Reproducible bam and reference files are below the error. Any ideas on how I should fix either file? Error: /pathTo/insurveyor-env/lib/python3.12/site-packages/numpy/_core/fromnumeric.py:3859: RuntimeWarning: Mean of empty slice. return _methods._mean(a, axis=axis, dtype=dtype, /pathTo/insurveyor-env/lib/python3.12/site-packages/numpy/_core/_methods.py:144: RuntimeWarning: invalid value encountered in scalar divide ret = ret.dtype.type(ret / rcount) /pathTo/insurveyor-env/lib/python3.12/site-packages/numpy/_core/_methods.py:222: RuntimeWarning: Degrees of freedom <= 0 for slice ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, /pathTo/insurveyor-env/lib/python3.12/site-packages/numpy/_core/_methods.py:180: RuntimeWarning: invalid value encountered in divide arrmean = um.true_divide(arrmean, div, out=arrmean, /pathTo/insurveyor-env/lib/python3.12/site-packages/numpy/_core/_methods.py:214: RuntimeWarning: invalid value encountered in scalar divide ret = ret.dtype.type(ret / rcount) Traceback (most recent call last): File "/pathTo/insurveyor-env/bin/insurveyor.py", line 119, in <module> avg_depth = float(avg_depth)/samplings ~~~~~~~~~~~~~~~~^~~~~~~~~~ ZeroDivisionError: float division by zero Aligned reads (bam): @HD VN:1.5 SO:coordinate @SQ SN:CK-TSC14 LN:11114 @RG ID:250609_Align_ck-tsc14_ACR_tsc_tDG_1 SM:250609_Align_ck-tsc14_ACR_tsc_tDG_1 @PG ID:bwa PN:bwa VN:0.7.18-r1243-dirty CL:bwa mem -Y -M -R @RG\tID:250609_Align_ck-tsc14_ACR_tsc_tDG_1\tSM:250609_Align_ck-tsc14_ACR_tsc_tDG_1 -t 8 reference/ref.fa pathTo/reads_R1_001.fastq.gz pathTo/reads_R2_001.fastq.gz @PG ID:samtools PN:samtools PP:bwa VN:1.20 CL:samtools sort -n -l 0 -T /tmp --threads 3 -m 2000M @PG ID:samtools.1 PN:samtools PP:samtools VN:1.20 CL:samtools fixmate -m --threads 3 - - @PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:samtools sort -l 0 -T /tmp --threads 3 -m 2000M @PG ID:samtools.3 PN:samtools PP:samtools.2 VN:1.20 CL:samtools markdup -T /tmp --threads 3 -r -s - - LH00162:272:22VH25LT4:8:1383:42550:9435 99 CK-TSC14 511 60 148M = 609 248 GATTTAAATACTAGTGTTAACTATTTAATTGGGGACCCTAGAGGTCCCCTTTTTTATTTTAAAAATTTTTTCAAGGGGACCTCTAGGGTCCCCAGCTGGCTAGCGAGTCATGAGGTCACCATGTTCTTTCCTGCGTTATCCCCTGATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:148 AS:i:148 XS:i:22 RG:Z:250609_Align_ck-tsc14_ACR_tsc_tDG_1 MQ:i:60 MC:Z:150M ms:i:6000 LH00162:272:22VH25LT4:8:2161:6890:4391 64 CK-TSC14 512 60 147M * 0 0 GTTTAAATACTAGTGTTAACTATTTAATTGGGGACCCTAGAGGTCCCCTTTTTTATTTTAAAAATTTTTTCCAGGGGACCTCTAGGGTCCCCAGCTGGCTCGCGAGTCATGAGGTCACCCTGTTCTTTCCTGCGTTATCCCCTGATT **9*99I9IIIIII9II*9II9IIII*II*III*I9II9I*IIIIIIIII9III9II999*I*9IIIIIII*I*I9**I9III9II9I9III*9I*II9I9II*I*9III9*IIIII9I*99*9IIIII9IIIIIIII9II9IIII9 NM:i:4 MD:Z:0A70A28A18A27 MC:Z:89S59M MQ:i:39 AS:i:131 XS:i:32 RG:Z:250609_Align_ck-tsc14_ACR_tsc_tDG_1 LH00162:272:22VH25LT4:8:2425:23879:9996 64 CK-TSC14 513 60 151M * 0 0 GTTAAATACTAGTGTTAACTATTTAATTGGGGACCCTAGAGGTCCCCTTTTTTATTTTAAAAATTTTTTCAAGGGGACCTCTAGGGTCCCCAGCTGGCTAGCGAGTCATGAGGTCACCATGTTCTTTCCTGCGTTATCCCCTGATTCTGTG **9*999I99III9*9III9I9II9IIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIII9IIIIIIIIIIIIIII9IIIIIIIIII9IIIIIII9IIIII9I9IIIIIIII*II99III*99I*9*I9I99I9IIIIII9IIIII9IIII NM:i:1 MD:Z:0T150 MC:Z:116S35M MQ:i:60 AS:i:150 XS:i:22 RG:Z:250609_Align_ck-tsc14_ACR_tsc_tDG_1 LH00162:272:22VH25LT4:8:1213:9114:8917 163 CK-TSC14 516 60 151M = 587 221 AAATACTAGTGTTAACTATTTAATTGGGGACCCTAGAGGTCCCCTTTTTTATTTTAAAAATTTTTTCAAGGGGACCTCTAGGGTCCCCAGCTGGCTAGCGAGTCATGAGGTCACCATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 MD:Z:151 AS:i:151 XS:i:22 RG:Z:250609_Align_ck-tsc14_ACR_tsc_tDG_1 MQ:i:60 MC:Z:150M ms:i:5984 Reference fasta >CK-TSC14 TCTTCCAAACTAGCTACGCGGGTTCGATTCCCGTCGCCCGCTCCGCTGGTCAGAGGGTGTTTTCGCCCTCTGGCCATTT TTCTTTCCAGGGGTCTGCAACTCTTGTGCGACTCTTCTGACCTGGGCATACGCGGTTGCAACGCATCCCTGATCTGGCT ACTTTCGATGCTGACAAACGAATAGAGCCCCCCGCCTGCGCGAACAGACGAGGGGCATTCACACCAGATTGGAGCTGGT GCAGTGAAGAGAATAGACCGGGACAAGGTTGCACCGGGAGTTGCAGCGGTCGGAACCCTCGCCGTCGGCGGGCTGGCGT TCGCCCTGTCGTTCACGGCTCTAGCAACAACAGATAAAACGAAAGGCCCAGTCTTTCGATGATCACCGCGGCCATGATG GCATAAAACGAAAGGCCCAGTCTTTCGACTGAGCCTTTCGTTTTATTTGATGCCTGGCAGTCGATCGTACGCTAGTTAA CTACGTCGACATCGATTTAATTAATATGCATCAATTGATTTAAATACTAGTGTTAACTATTTAATTGGGGACCCTAGAG GTCCCCTTTTTTATTTTAAAAATTTTTTCAAGGGGACCTCTAGGGTCCCCAGCTGGCTAGCGAGTCATGAGGTCACCAT GTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCAGCGGATAACAA Continue reading...
