Open SodiumJu opened 2 years ago
Hi there,
First, to help us debug, you may consider rerunning using the --debug
command. For each of the individual scaffolds, do the AGP files indicate any scaffolding? Or do the individual AGP files also leave everything unplaced?
Thanks
For each of the individual scaffolds, the AGP files do scaffold (as below).
## agp-version 2.1
# AGP created by RagTag v2.1.0
gi|444355692|ref|NZ_ALIZ01000001.1|_RagTag 1 3076 1 W 9499 1 3076 -
gi|444355700|ref|NZ_ALIZ01000002.1|_RagTag 1 3672 1 W 9425 1 3672 -
gi|444355706|ref|NZ_ALIZ01000003.1|_RagTag 1 7540 1 W 10234 1 7540 -
gi|444355716|ref|NZ_ALIZ01000004.1|_RagTag 1 6987 1 W 10165 1 6987 -
gi|444355716|ref|NZ_ALIZ01000004.1|_RagTag 6988 7087 2 U 100 scaffold yes align_genus
gi|444355716|ref|NZ_ALIZ01000004.1|_RagTag 7088 14523 3 W 10340 1 7436 -
gi|444355716|ref|NZ_ALIZ01000004.1|_RagTag 14524 14623 4 U 100 scaffold yes align_genus
gi|444355716|ref|NZ_ALIZ01000004.1|_RagTag 14624 17068 5 W 9462 1 2445 -
gi|444355741|ref|NZ_ALIZ01000006.1|_RagTag 1 3652 1 W 4832 1 3652 -
gi|444355760|ref|NZ_ALIZ01000009.1|_RagTag 1 2444 1 W 9847 1 2444 +
gi|444355760|ref|NZ_ALIZ01000009.1|_RagTag 2445 2544 2 U 100 scaffold yes align_genus
gi|444355760|ref|NZ_ALIZ01000009.1|_RagTag 2545 5352 3 W 9626 1 2808 +
gi|444355769|ref|NZ_ALIZ01000010.1|_RagTag 1 8294 1 W 4001 1 8294 +
gi|444355791|ref|NZ_ALIZ01000012.1|_RagTag 1 4562 1 W 9406 1 4562 -
gi|444355791|ref|NZ_ALIZ01000012.1|_RagTag 4563 4662 2 U 100 scaffold yes align_genus
gi|444355791|ref|NZ_ALIZ01000012.1|_RagTag 4663 6941 3 W 3482 1 2279 -
gi|444355800|ref|NZ_ALIZ01000013.1|_RagTag 1 4718 1 W 9718 1 4718 -
gi|444355807|ref|NZ_ALIZ01000014.1|_RagTag 1 5308 1 W 9872 1 5308 -
gi|444355813|ref|NZ_ALIZ01000015.1|_RagTag 1 3717 1 W 9797 1 3717 +
gi|444355813|ref|NZ_ALIZ01000015.1|_RagTag 3718 3817 2 U 100 scaffold yes align_genus
gi|444355813|ref|NZ_ALIZ01000015.1|_RagTag 3818 8002 3 W 9653 1 4185 +
gi|444355813|ref|NZ_ALIZ01000015.1|_RagTag 8003 8102 4 U 100 scaffold yes align_genus
gi|444355813|ref|NZ_ALIZ01000015.1|_RagTag 8103 13650 5 W 9079 1 5548 +
gi|444355813|ref|NZ_ALIZ01000015.1|_RagTag 13651 13750 6 U 100 scaffold yes align_genus
gi|444355813|ref|NZ_ALIZ01000015.1|_RagTag 13751 18516 7 W 1427 1 4766 -
gi|444355841|ref|NZ_ALIZ01000016.1|_RagTag 1 1485 1 W 9417 1 1485 -
gi|444355841|ref|NZ_ALIZ01000016.1|_RagTag 1486 1585 2 U 100 scaffold yes align_genus
I used the --debug command.
placed_sequences placed_bp unplaced_sequences unplaced_bp gap_bp gap_sequences
1221 7059333 2 5184 68500 685
Fri Dec 3 11:43:06 2021 --- VERSION: RagTag v2.1.0
Fri Dec 3 11:43:06 2021 --- CMD: ragtag.py scaffold -u --debug -o out_1 ../../datasets/BCEN/reference_genomes/Burkholderia_cenocepacia_BC7_uid188101.fasta ../../datasets/BCEN/Burkholderia_target.fasta
Fri Dec 3 11:43:06 2021 --- INFO: Mapping the query genome to the reference genome
Fri Dec 3 11:43:06 2021 --- INFO: Running: minimap2 -x asm5 -t 1 /home/genome/Test_MultiCSAR/datasets/BCEN/reference_genomes/Burkholderia_cenocepacia_BC7_uid188101.fasta /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.asm.paf 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.asm.paf.log
Fri Dec 3 11:43:06 2021 --- INFO: Finished running : minimap2 -x asm5 -t 1 /home/genome/Test_MultiCSAR/datasets/BCEN/reference_genomes/Burkholderia_cenocepacia_BC7_uid188101.fasta /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.asm.paf 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.asm.paf.log
Fri Dec 3 11:43:06 2021 --- INFO: Reading whole genome alignments
Fri Dec 3 11:43:06 2021 --- INFO: Filtering and merging alignments
Fri Dec 3 11:43:06 2021 --- INFO: Ordering and orienting query sequences
Fri Dec 3 11:43:06 2021 --- INFO: Writing scaffolds
Fri Dec 3 11:43:06 2021 --- INFO: Writing: /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.agp
Fri Dec 3 11:43:06 2021 --- INFO: Running: ragtag_agp2fa.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.fasta 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.err
Fri Dec 3 11:43:06 2021 --- INFO: Finished running : ragtag_agp2fa.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.fasta 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.err
Fri Dec 3 11:43:06 2021 --- INFO: Running: ragtag_stats.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.confidence.txt > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.stats 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.err
Fri Dec 3 11:43:06 2021 --- INFO: Finished running : ragtag_stats.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.confidence.txt > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.stats 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_1/ragtag.scaffold.err
Fri Dec 3 11:43:06 2021 --- INFO: Goodbye
placed_sequences placed_bp unplaced_sequences unplaced_bp gap_bp gap_sequences
1166 6626117 57 438400 110900 1109
0971.fasta ../../datasets/BCEN/Burkholderia_target.fasta
Fri Dec 3 11:43:44 2021 --- VERSION: RagTag v2.1.0
Fri Dec 3 11:43:44 2021 --- CMD: ragtag.py scaffold -u --debug -o out_2 ../../datasets/BCEN/reference_genomes/Burkholderia_cenocepacia_H111_uid180971.fasta ../../datasets/BCEN/Burkholderia_target.fasta
Fri Dec 3 11:43:44 2021 --- INFO: Mapping the query genome to the reference genome
Fri Dec 3 11:43:44 2021 --- INFO: Running: minimap2 -x asm5 -t 1 /home/genome/Test_MultiCSAR/datasets/BCEN/reference_genomes/Burkholderia_cenocepacia_H111_uid180971.fasta /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.asm.paf 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.asm.paf.log
Fri Dec 3 11:43:44 2021 --- INFO: Finished running : minimap2 -x asm5 -t 1 /home/genome/Test_MultiCSAR/datasets/BCEN/reference_genomes/Burkholderia_cenocepacia_H111_uid180971.fasta /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.asm.paf 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.asm.paf.log
Fri Dec 3 11:43:44 2021 --- INFO: Reading whole genome alignments
Fri Dec 3 11:43:44 2021 --- INFO: Filtering and merging alignments
Fri Dec 3 11:43:44 2021 --- INFO: Ordering and orienting query sequences
Fri Dec 3 11:43:44 2021 --- INFO: Writing scaffolds
Fri Dec 3 11:43:44 2021 --- INFO: Writing: /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.agp
Fri Dec 3 11:43:44 2021 --- INFO: Running: ragtag_agp2fa.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.fasta 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.err
Fri Dec 3 11:43:44 2021 --- INFO: Finished running : ragtag_agp2fa.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.fasta 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.err
Fri Dec 3 11:43:44 2021 --- INFO: Running: ragtag_stats.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.confidence.txt > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.stats 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.err
Fri Dec 3 11:43:45 2021 --- INFO: Finished running : ragtag_stats.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.confidence.txt > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.stats 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_2/ragtag.scaffold.err
Fri Dec 3 11:43:45 2021 --- INFO: Goodbye
placed_sequences placed_bp unplaced_sequences unplaced_bp gap_bp gap_sequences
1183 6818960 40 245557 71000 710
no_uid188102.fasta ../../datasets/BCEN/Burkholderia_target.fasta
Fri Dec 3 11:44:21 2021 --- VERSION: RagTag v2.1.0
Fri Dec 3 11:44:21 2021 --- CMD: ragtag.py scaffold -u --debug -o out_3 ../../datasets/BCEN/reference_genomes/Burkholderia_cenocepacia_K56_2Valvano_uid188102.fasta ../../datasets/BCEN/Burkholderia_target.fasta
Fri Dec 3 11:44:21 2021 --- INFO: Mapping the query genome to the reference genome
Fri Dec 3 11:44:21 2021 --- INFO: Running: minimap2 -x asm5 -t 1 /home/genome/Test_MultiCSAR/datasets/BCEN/reference_genomes/Burkholderia_cenocepacia_K56_2Valvano_uid188102.fasta /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.asm.paf 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.asm.paf.log
Fri Dec 3 11:44:22 2021 --- INFO: Finished running : minimap2 -x asm5 -t 1 /home/genome/Test_MultiCSAR/datasets/BCEN/reference_genomes/Burkholderia_cenocepacia_K56_2Valvano_uid188102.fasta /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.asm.paf 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.asm.paf.log
Fri Dec 3 11:44:22 2021 --- INFO: Reading whole genome alignments
Fri Dec 3 11:44:22 2021 --- INFO: Filtering and merging alignments
Fri Dec 3 11:44:22 2021 --- INFO: Ordering and orienting query sequences
Fri Dec 3 11:44:22 2021 --- INFO: Writing scaffolds
Fri Dec 3 11:44:22 2021 --- INFO: Writing: /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.agp
Fri Dec 3 11:44:22 2021 --- INFO: Running: ragtag_agp2fa.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.fasta 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.err
Fri Dec 3 11:44:22 2021 --- INFO: Finished running : ragtag_agp2fa.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.fasta 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.err
Fri Dec 3 11:44:22 2021 --- INFO: Running: ragtag_stats.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.confidence.txt > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.stats 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.err
Fri Dec 3 11:44:22 2021 --- INFO: Finished running : ragtag_stats.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.confidence.txt > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.stats 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_3/ragtag.scaffold.err
Fri Dec 3 11:44:22 2021 --- INFO: Goodbye
placed_sequences placed_bp unplaced_sequences unplaced_bp gap_bp gap_sequences
1044 6016154 179 1048363 104100 1041
Fri Dec 3 11:44:48 2021 --- VERSION: RagTag v2.1.0
Fri Dec 3 11:44:48 2021 --- CMD: ragtag.py scaffold -u --debug -o out_4 ../../datasets/BCEN/reference_genomes/Burkholderia_cenocepacia_PC184_uid54353.fasta ../../datasets/BCEN/Burkholderia_target.fasta
Fri Dec 3 11:44:48 2021 --- INFO: Mapping the query genome to the reference genome
Fri Dec 3 11:44:48 2021 --- INFO: Running: minimap2 -x asm5 -t 1 /home/genome/Test_MultiCSAR/datasets/BCEN/reference_genomes/Burkholderia_cenocepacia_PC184_uid54353.fasta /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.asm.paf 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.asm.paf.log
Fri Dec 3 11:44:49 2021 --- INFO: Finished running : minimap2 -x asm5 -t 1 /home/genome/Test_MultiCSAR/datasets/BCEN/reference_genomes/Burkholderia_cenocepacia_PC184_uid54353.fasta /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.asm.paf 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.asm.paf.log
Fri Dec 3 11:44:49 2021 --- INFO: Reading whole genome alignments
Fri Dec 3 11:44:49 2021 --- INFO: Filtering and merging alignments
Fri Dec 3 11:44:49 2021 --- INFO: Ordering and orienting query sequences
Fri Dec 3 11:44:49 2021 --- INFO: Writing scaffolds
Fri Dec 3 11:44:49 2021 --- INFO: Writing: /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.agp
Fri Dec 3 11:44:49 2021 --- INFO: Running: ragtag_agp2fa.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.fasta 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.err
Fri Dec 3 11:44:49 2021 --- INFO: Finished running : ragtag_agp2fa.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.fasta 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.err
Fri Dec 3 11:44:49 2021 --- INFO: Running: ragtag_stats.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.confidence.txt > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.stats 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.err
Fri Dec 3 11:44:49 2021 --- INFO: Finished running : ragtag_stats.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.agp /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.confidence.txt > /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.stats 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/out_4/ragtag.scaffold.err
Fri Dec 3 11:44:49 2021 --- INFO: Goodbye
Fri Dec 3 11:45:45 2021 --- VERSION: RagTag v2.1.0
Fri Dec 3 11:45:45 2021 --- WARNING: This is a beta version of `ragtag merge`
Fri Dec 3 11:45:45 2021 --- CMD: ragtag.py merge -u --debug ../../datasets/BCEN/Burkholderia_target.fasta out_1/ragtag.scaffold.agp out_2/ragtag.scaffold.agp out_3/ragtag.scaffold.agp out_4/ragtag.scaffold.agp
Fri Dec 3 11:45:45 2021 --- INFO: Building the scaffold graph from the AGP files
Fri Dec 3 11:45:45 2021 --- INFO: Merging the scaffold graph
Fri Dec 3 11:45:45 2021 --- INFO: Computing a scaffolding solution
Fri Dec 3 11:45:45 2021 --- INFO: Writing results
Fri Dec 3 11:45:45 2021 --- INFO: Running: ragtag_agp2fa.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/ragtag_output/ragtag.merge.agp ../../datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/ragtag_output/ragtag.merge.fasta 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/ragtag_output/ragtag.merge.err
Fri Dec 3 11:45:45 2021 --- INFO: Finished running : ragtag_agp2fa.py /home/genome/Test_MultiCSAR/Ragtag/BCEN/ragtag_output/ragtag.merge.agp ../../datasets/BCEN/Burkholderia_target.fasta > /home/genome/Test_MultiCSAR/Ragtag/BCEN/ragtag_output/ragtag.merge.fasta 2> /home/genome/Test_MultiCSAR/Ragtag/BCEN/ragtag_output/ragtag.merge.err
Fri Dec 3 11:45:45 2021 --- INFO: Goodbye
Thank you.
For each step, there is nothing left in *.err file.
By the way, the sample is from B.cenocepacia j2315 in Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lio P, et al. MeDuSa: A multi-draft based scaffolder. Bioinformatics. 2015;31:2443-2451
Thanks so much for the details. I can't see any obvious problems, so would you be willing to share the data so that I could take a look myself? If so, you can send the data (or info on where to find it) to malonge11@gmail.com
Thanks so much for the help. The link below it's the testing data. https://drive.google.com/drive/folders/167FfRBn3DPH_OYDY7o01eH4jWG-Hlxdx?usp=sharing
I used the commands as below to scaffold my target.fasta with four reference files.
It successfully scaffolds the target file with the reference file respectively and the results are also normal. However, the result generated by merge is strange (shown as below). The merged result agp file only contains contigs from target file without scaffolding.
I hope you will be able to provide the information to fix the problem. Thank you.