Open suvi93 opened 8 months ago
Hi Suvi, could you tell me what your input file and the command you use are? It seems that the input file doesn't match the command.
Best, Peng
Hi Peng,
here is the command i used -
CUDA_VISIBLE_DEVICES=0,1 ccsmeth call_mods \ --input hifi-kinetics_out/Vv19_2.fofn \ #file containing hifi kinetics bam files --ref ref/Vv19/vv19.fa \ --model_file ccsmeth/models/model_ccsmeth_5mCpG_call_mods_attbigru2s_b21.v2.ckpt \ --output Vv19.hifi.modbam.bam \ --threads 15 --threads_call 2 --model_type attbigru2s \ --mode align
Hi @suvi93 , the --input
param should be a bam file, not the fofn file. Please try again, if there are any issues, please feel free to concat me.
Best, Peng
Hi Peng,
so i have 5 different kinetics bam file for the same sample, so if i process them individually can i concatenate all the results of the pipeline at the end?
Thanks, Suvi
Yes Suvi, you can use samtools to merge all the output bam files.
Hi Peng,
is there a way to change the indexing of the bam files from samtools index to bamtools index or to split the bam file and then run the indexing? my bam file is too huge to be indexed with samtools index and this is the error i get -
2024-02-02 11:28:34 - INFO - [main]align_hifi_reads starts 2024-02-02 11:28:34 - INFO - cmds: pbmm2 align --preset CCS -j 15 --sort vv19.fa m64077_220928_112919.hifi.modbam.bam m64077_220928_112919.hifi.call_mods.modbam.pbmm2.bam && samtools index -@ 15 m64077_220928_112919.hifi.call_mods.modbam.pbmm2.bam 2024-02-02 14:32:58 - WARNING - failed.. 2024-02-02 14:32:59 - INFO - stdout:
2024-02-02 14:32:59 - INFO - stderr: |> 20240202 10:28:34.527 -|- WARN -|- operator() -|- 0x2b19e1f6c340|| -|- Input is aligned reads. Only primary alignments will be respected to allow idempotence! [E::hts_idx_check_range] Region 536859611..536871025 cannot be stored in a bai index. Try using a csi index [E::sam_index] Read 'm64077_220928_112919/142936459/ccs' with ref_name='scaffold_1', ref_length=591107699, flags=16, pos=536859612 cannot be indexed |> 20240202 13:32:54.623 -|- FATAL -|- Close -|- 0x2b19e1f6c340|| -|- pbmm2 align ERROR: BAI Index Generation: Failed to create index for m64077_220928_112919.hifi.call_mods.modbam.pbmm2.bam
Hi @suvi93 , I am not sure, but maybe you can try samtools index
with --csi
option.
Best, Peng
in which script do I add the --csi
option?
sorry, that part was a bit unclear as nowhere in the command for align_hifi am I mentioning this -
ccsmeth align_hifi --hifireads m64077_220928_112919.hifi.modbam.bam --ref vv19.fa --output m64077_220928_112919.hifi.call_mods.modbam.pbmm2.bam --threads 15
Hi PengNi, I encountered a similar indexing issue. My bam file cannot be bai indexed. I used samtools index -c for csi index. However, ccsmeth call_mods still starts with bai indexing step despite the existing csi index. How to skip this step? Thanks
Hi PengNi, I encountered a similar indexing issue. My bam file cannot be bai indexed. I used samtools index -c for csi index. However, ccsmeth call_mods still starts with bai indexing step despite the existing csi index. How to skip this step? Thanks
Hi @zihaozhu92 , did you use the latest version of ccsmeth?
I'm getting the following error and after this the job seems to be idling. it does not exit out and give me an error but instead keeps running without producing an output. the error is below -
how do i go about fixing the index error as it says?
thanks, Suvi