Errors on idxdepth

[Yexin-Zhang]

Hi,

I am trying to use the idxdepth to calculate the depth for the manifest file, but it always gives me a warning:

[warning] BAM header only has a subset of the reference chromosomes -- please make sure they match!

The issues falls on many datasets that I tried. I use bwa for alignment, and gatk for read groups adding/duplicates removing.

Any hint for how might this happened?

Best,
Monica

[traxexx]

This is a bam header error. Did you use the same reference fasta for generating your bam, and for running idxdepth?

[biozzq]

Hi @traxexx

Yes, even I use the same reference fasta for generating BAM files, it sometimes give me the errors.

Best regards,
Zheng zhuqing

[karen916]

Hello,@traxexx

I have encountered the same issue. Using the same reference genome, I came across the following warning message:

[2023-11-05 16:25:41.063] [idxdepth] [48575] [warning] BAM header only has a subset of the reference chromosomes -- please make sure they match!
The command I used is as follows:

(py37) [chenzhaojin@lfpara idxdepth]$ idxdepth -b /home/chenzhaojin/expansion/sv/results_1-6_supdata1/1-12/delly/alignment_1_sorted.bam
-o /home/chenzhaojin/expansion/sv/results_1-6_supdata1/paragraph/idxdepth/depth_1-12.txt
-O /home/chenzhaojin/expansion/sv/results_1-6_supdata1/paragraph/idxdepth/depth_1-12_tsv.txt
-r /home/chenzhaojin/sv_test/GCF_000003025.6_Sscrofa11.1_genomic.fna
--threads 48
My BAM file was generated by bwa mem. Upon checking the logs, I noticed many chromosome segments being skipped, with parts of the log as follows:

[2023-11-05 16:25:41.741] [idxdepth] [48591] [info] Thread 140667879675648 skipping NC_010443.5
[2023-11-05 16:25:41.741] [idxdepth] [48591] [info] Thread 140667879675648 skipping NC_010445.4
... (and so on for the rest of the chromosomes)
Running the samtools view command again to inspect the file header, it appears that these chromosome identifiers do exist:
(py37) [chenzhaojin@lfpara delly]$ samtools view -H alignment_1_sorted.bam
@hd VN:1.3 SO:coordinate
@sq SN:NC_010443.5 LN:274330532
... (and so on for the rest of the chromosomes)
Could you please help me understand why idxdepth is skipping these chromosome segments even though they are present in the BAM header? What could be causing this discrepancy?
In addition, I encountered a similar issue when running the command:
python3 /home/chenzhaojin/tools/bin/multigrmpy.py -i /home/chenzhaojin/expansion/sv/results_1-6_supdata1/survivor/filter1_DEL.vcf
-m /home/chenzhaojin/expansion/sv/results_1-6_supdata1/paragraph/samples.txt
-t 48
-r /home/chenzhaojin/expansion/sv/mid75/paragraph/GCF_000003025.6_Sscrofa11.1_genomic_uppercase.fna
-o test1
The error message was:

Exception: NC_010443.5:75954757 fail to retrieve genome REF. Are you using the correct ref genome?
Could this issue be related to the previous one, and how can I ensure that the reference genome is correctly recognized in both cases?
Thank you for your assistance.