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malonge / RagTag

Tools for fast and flexible genome assembly scaffolding and improvement
MIT License
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Multiple reference issue #91

Open SodiumJu opened 2 years ago

SodiumJu commented 2 years ago

I used the commands as below to scaffold my target.fasta with four reference files.

ragtag.py scaffold -u -o out_1 <path>/reference_genomes/Burkholderia_cenocepacia_PC184_uid54353.fasta <path>/BCEN/Burkholderia_target.fasta
ragtag.py scaffold -u -o out_2 <path>/reference_genomes/Burkholderia_cenocepacia_K56_2Valvano_uid188102.fasta <path>/Burkholderia_target.fasta
ragtag.py scaffold -u -o out_3 <path>/reference_genomes/Burkholderia_cenocepacia_H111_uid180971.fasta <path>/Burkholderia_target.fasta
ragtag.py scaffold -u -o out_4 <path>/reference_genomes/Burkholderia_cenocepacia_BC7_uid188101.fasta <path>/Burkholderia_target.fasta

ragtag.py merge -u <path>/Burkholderia_target.fasta out_*/*.agp

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.

9114_RagTag     1       44607   1       W       9114    1       44607   +
10360_RagTag    1       8275    1       W       10360   1       8275    +
9180_RagTag     1       2388    1       W       9180    1       2388    +
10184_RagTag    1       16078   1       W       10184   1       16078   +
9538_RagTag     1       1396    1       W       9538    1       1396    +
10066_RagTag    1       9133    1       W       10066   1       9133    +
10225_RagTag    1       1621    1       W       10225   1       1621    +
3264_RagTag     1       2531    1       W       3264    1       2531    +
9219_RagTag     1       1825    1       W       9219    1       1825    +
9347_RagTag     1       3140    1       W       9347    1       3140    +
9870_RagTag     1       1464    1       W       9870    1       1464    +
9650_RagTag     1       8741    1       W       9650    1       8741    +
10068_RagTag    1       4893    1       W       10068   1       4893    +
9396_RagTag     1       1699    1       W       9396    1       1699    +
6705_RagTag     1       1340    1       W       6705    1       1340    +
10143_RagTag    1       5068    1       W       10143   1       5068    +
9642_RagTag     1       1591    1       W       9642    1       1591    +
9582_RagTag     1       2371    1       W       9582    1       2371    +
9125_RagTag     1       4104    1       W       9125    1       4104    +
5007_RagTag     1       6700    1       W       5007    1       6700    +
9404_RagTag     1       2218    1       W       9404    1       2218    +
10388_RagTag    1       3637    1       W       10388   1       3637    +
9547_RagTag     1       8924    1       W       9547    1       8924    +
10296_RagTag    1       1424    1       W       10296   1       1424    +
10108_RagTag    1       1752    1       W       10108   1       1752    +
10262_RagTag    1       17923   1       W       10262   1       17923   +
9424_RagTag     1       4349    1       W       9424    1       4349    +
9814_RagTag     1       3111    1       W       9814    1       3111    +
9983_RagTag     1       5576    1       W       9983    1       5576    +
9639_RagTag     1       2367    1       W       9639    1       2367    +
9913_RagTag     1       2977    1       W       9913    1       2977    +
10310_RagTag    1       7336    1       W       10310   1       7336    +
9880_RagTag     1       8997    1       W       9880    1       8997    +
9963_RagTag     1       8178    1       W       9963    1       8178    +
9874_RagTag     1       6204    1       W       9874    1       6204    +
10231_RagTag    1       10886   1       W       10231   1       10886   +
...

I hope you will be able to provide the information to fix the problem. Thank you.

malonge commented 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

SodiumJu commented 2 years ago

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
SodiumJu commented 2 years ago

I used the --debug command.

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
  1. out_2 ragtag.scaffold.stats 
    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
  1. out_3 ragtag.scaffold.stats 
    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
  1. out_4 ragtag.scaffold.stats 
    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

Thank you.

SodiumJu commented 2 years ago

For each step, there is nothing left in *.err file.

SodiumJu commented 2 years ago

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

malonge commented 2 years ago

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

SodiumJu commented 2 years ago

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