peterstockwell
commented
1 year ago Hi
The genome sequence need to be fasta, I suspect that diffmeth is not finding an appropriate header line. Also the -G diffmeth option should be getting a list of files and appropriate chromosome IDs. If the original fasta sequence file is processed by the dmap_index_build.sh then the file given to the diffmeth -G option should be properly formatted.
Could you please email to me your basic parameter file which would have been the argument to the
dmap_index_build.sh
script.
Could you also email the ./genome_top100.fasta file.
Regards Peter Stockwell
From: Magdalena @.> Sent: Friday, July 28, 2023 10:12 PM To: peterstockwell/DMAP2 @.> Cc: Subscribed @.***> Subject: [peterstockwell/DMAP2] Error: "Need genome sequence file header string" (Issue #1)
Hi,
I am working with WGBS data and would like to use DMAP2 to investigate the differences in DMA methylation. Since I am working with a non-model organism our genome is not very polished and still work-in-progress (it is not published yet, so I can't download anything from ensembl). I have a .fasta genome file with the whole genome (not separated in chromosomes) and a .gtf annotation file. I have performed the alignment in Bismark and got 12 .bam files (4 samples in 3 groups). I filled the "dmap_basic_params.conf" and "dmap_anova3_params.conf" with the needed information about the directories to find the corresponding files, but I couldn't get the program started. I can see that DMAP2 finds the working directory, the two config files, and the three groups with all my samples, and than I get: "Executing: ./DMAP/src/diffmeth -G ./genome_top100.fasta -W 1000 -t 10 -I 6 -B 40,220 -z -R1 ./1-N1-D14-1_S1_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R1 ./2-N2-D15-1_S8_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R1 ./3-N3-D16-2_S4_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R1 ./4-N7-D36-1_S5_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R2 ./5-A1-D17-1_S9_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R2 ./6-A2-D18-1_S3_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R2 ./7-A4-D26-2_S7_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R2 ./8-A7-D37-1_S11_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R3 ./9-24R2-D21-2_S6_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R3 ./10-24R3-D22-2_S2_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R3 ./11-24R7-D21-2_S6_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R3 ./12-24R8-D22-2_S2_L001_R1_001_val_1_bismark_bt2_pe.bam > ./diffmeth_output_anova3.txt Need genome sequence file header string"
I removed sensible information and added spaces to make it more readable.
What does "Need genome sequence file header string" mean? In the "dmap_basic_params.conf" file, I listed the genome "as a single file" with the absolute path.
Thank you for your help!!!
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MagdalenaWinklhofer
Hi,
I am working with WGBS data and would like to use DMAP2 to investigate the differences in DMA methylation. Since I am working with a non-model organism our genome is not very polished and still work-in-progress (it is not published yet, so I can't download anything from ensembl). I have a .fasta genome file with the whole genome (not separated in chromosomes) and a .gtf annotation file. I have performed the alignment in Bismark and got 12 .bam files (4 samples in 3 groups). I filled the "dmap_basic_params.conf" and "dmap_anova3_params.conf" with the needed information about the directories to find the corresponding files, but I couldn't get the program started. I can see that DMAP2 finds the working directory, the two config files, and the three groups with all my samples, and than I get: "Executing: ./DMAP/src/diffmeth -G ./genome_top100.fasta -W 1000 -t 10 -I 6 -B 40,220 -z -R1 ./1-N1-D14-1_S1_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R1 ./2-N2-D15-1_S8_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R1 ./3-N3-D16-2_S4_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R1 ./4-N7-D36-1_S5_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R2 ./5-A1-D17-1_S9_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R2 ./6-A2-D18-1_S3_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R2 ./7-A4-D26-2_S7_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R2 ./8-A7-D37-1_S11_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R3 ./9-24R2-D21-2_S6_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R3 ./10-24R3-D22-2_S2_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R3 ./11-24R7-D21-2_S6_L001_R1_001_val_1_bismark_bt2_pe.bam -z -R3 ./12-24R8-D22-2_S2_L001_R1_001_val_1_bismark_bt2_pe.bam > ./diffmeth_output_anova3.txt \ Need genome sequence file header string"
I removed sensible information and added spaces to make it more readable.
What does "Need genome sequence file header string" mean? In the "dmap_basic_params.conf" file, I listed the genome "as a single file" with the absolute path.
Thank you for your help!!!