One merged fa can't not map to 63 individual bam file

[Rhettbest]

Dear vRhyme author
Thanks for sharing this powerful tools. I have 63 samples and I merged all the 63 samples in to one file into clean.3.fa but I do not have the merged bam for clean.3.fa. So I tried the following code but it not working. I already tried single virus.fa to virus.bam and it works well. When it comes to the merged one, there is no bins output. Could you please help me?

My code is
source activate vRhyme
vRhyme -i /home/ampere/whuaiyu/JGI_cd_hit/CD_HIT_second/clean_renamed_cd_hit_checkv.out/Viral_53all_incomplete_noprovirus/VIBRANT_clean.2_incomplete/clean.3.fa -b /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/*.bam -t 32

The log file is
Command: /home/ampere/whuaiyu/anaconda3/envs/vRhyme/bin/vRhyme -i /home/ampere/whuaiyu/JGI_cd_hit/CD_HIT_second/clean_renamed_cd_hit_checkv.out/Viral_53all_incomplete_noprovirus/VIBRANT_clean.2_incomplete/clean.3.fa -b /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_10.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_11.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_12.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_13.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_14.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_16.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_17.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_18.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_19.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_1.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_20.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_21.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_22.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_23.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_24.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_26.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_27.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_29.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_2.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_30.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_31.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_32.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_33.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_34.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_35.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_36.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_37.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_38.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_39.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_3.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_40.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_41.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_42.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_43.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_44.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_45.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_46.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_47.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_48.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_49.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_4.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_50.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_51.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_52.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_53.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_54.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_55.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_56.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_57.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_58.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_59.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_5.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_60.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_61.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_62.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_63.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_64.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_65.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_66.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_6.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_7.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_8.bam /store/ampere/hwang/JGI_Viromic_analysis/Sam/bam_folder/Viral_MG_9.bam -t 32

Date: 2024-03-10 (y-m-d)
Start: 15:28:08 (h:m:s)
Program: vRhyme v1.1.0

Time (min) | Log

0.0 Initializing and validating vRhyme parameters
2.69 Extracting coverage information from BAM files
13.73 Coverage extraction complete. Generating coverage table
13.77 Performing pairwise coverage comparisons
13.87 vRhyme binning complete

Memory usage: 0.99
Runtime (min): 13.87
Bins generated: 0

[KrisKieft]

Without more information I'm not sure what may be happening. How many sequences are in your input fasta file? Does it look like the sequences have coverage across multiple samples? Is there any other information you can provide?

[Rhettbest]

Dear authorI am appreciate for your answer. This merged input fasta file contain 440,000 v OTU received from Virsorter and did redundancy. These vOTU have coverage across multiple samples. Bam files are 63 separated samples, I do not have a method to merge these bams, so I would like to find a method to bin this merged input file with 63 separate bam files.Thank you Best wishes HuaiyuSent from my iPhoneOn 29 Mar 2024, at 00:37, Kris Kieft ***@***.***> wrote: Without more information I'm not sure what may be happening. How many sequences are in your input fasta file? Does it look like the sequences have coverage across multiple samples? Is there any other information you can provide? —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>