The index file is older than the data file: alignment.sorted.bam.bai

[rl4940]

Hi Team: I got this error message which is kinda weird to me to be understood: I crop a portion of the log: `` 2024-05-18 08:35:25,380 [INFO] Finished chrUn_KI270442v1-chrUn_KI270589v1:TRA/BND. 2024-05-18 08:35:25,380 [INFO] Finished chrUn_KI270442v1-chrUn_KI270590v1:TRA/BND. 2024-05-18 08:35:25,380 [INFO] Finished chrUn_KI270442v1-chrUn_KI270756v1:TRA/BND. [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.csi [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.csi [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.csi

You see, there are threads running fine, in the mean time, some threads says this error...
And I changed to .bam.bai instead, but I got the same message:

[W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai Running Sniffles2, build 2.2 Run Mode: call_sample Start on: 2024/05/22 10:38:16 Working dir: /data/renqgli/project/TGS/pipeline/test_hg002_giab_hg19 Used command: /data/renqgli/miniconda3/bin/sniffles --threads 10 --input alignment.sorted.bam --vcf sniffles2_hg19_hg002.vcf --sample-id hg002 --reference /data/renqgli/project/refseq/hs37d5.fa --minsvlen 50

Opening for reading: alignment.sorted.bam Opening for reading: /data/renqgli/project/refseq/hs37d5.fa Opening for writing: sniffles2_hg19_hg002.vcf (single-sample, sorted) [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai[W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.baiThe index file is older than the data file: alignment.sorted.bam.bai[W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai

The index file is older than the data file: alignment.sorted.bam.bai

[W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data 2024-05-22 10:39:16,934 [INFO ] Processed read 240000 2024-05-22 10:41:08,464 [INFO ] Processed read 250000 2024-05-22 10:42:59,035 [INFO ] Processed read 260000 data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai [W::hts_idx_load3] The index file is older than the data file: alignment.sorted.bam.bai

Btw, my .bam.bai generated code is downblow (I am writing a pipeline):

>>> Part I intiates: requirments: minimap2, samtools, fastq files, reference genome <<<

fastqgz_all='' for fn in *.fastq.gz; do fastqgz_all=${fn}' '${fastqgz_all}; done fastqgz_all="${fastqgz_all%" "}" # Trim trailing space at the end of string echo "#######-- pipeline start --#######" minimap2 -ax map-ont --secondary=no --MD -t 18 $ref $fastqgz_all
|samtools sort -O BAM --write-index -o alignment.sorted.bam##idx##alignment.sorted.bam.bai - echo "#######-- Calculate End Time:date +%Y/%m/%d--%H:%M --#######"

>>> Part I ends: output: alignment.sorted.bam <<<

Thank you for your help