Hi,

I tried using REPdenovo and it works fine until merging the different kmer velvet assemblies. While I have 394528 sequences in the contigs.fa_no_dup.fa file, all following merged files and the resulting contigs.fa file is empty. It seems like something in the pipeline is not working correctly.

Any thoughts?

Best,

Philipp

Hi,
I'm student in intership in a Lab in France.
So i rread many times your review while my bibliography project.
So now i'm testing your tool and i get some problem.
Please find the output error
output_error.txt

my config file
config_file.txt

and the readfile
read_file_1.txt

Thanks you

Hello. I use short reads from http://www.ebi.ac.uk/ena/data/view/SRX040486 as input (RepARK paper data),
sample_configuration_10X.txt
reads.txt

and for the configuration and read txt, I use the settings and the running log as denovo.txt as the attachment. But the result file is only 60k, I think I may set something wrong. Can you have a look at those file? Especially I do not know how to set the information about insert. Thanks!

Hi,

I'm trying to get REPdeonovo working on my system but I am coming across errors, such as the one below.

I've used python 2.6.6 and python 2.7.3 and I have all the dependencies installed byt when I run main.py I get the following error.

[shabanb@melb-compute05 121]$ python /data/Bioinfo/bioinfo-proj-bobbie/newProgs/REPdenovo/main.py -c Assembly -g config.txt -r file.txt
rm: cannot remove ./repdenovo/Asm_*': No such file or directory rm -r ./repdenovo/Asm_* rm ./repdenovo/*.fa rm: cannot remove./repdenovo/.fastq': No such file or directory
rm ./repdenovo/.fastq
Working on 30mer now...
Highest 30mer frequency is 0
Traceback (most recent call last):
File "/data/Bioinfo/bioinfo-proj-bobbie/newProgs/REPdenovo/main.py", line 397, in
main_func(scommand,sfconfig,sfreads_list)
File "/data/Bioinfo/bioinfo-proj-bobbie/newProgs/REPdenovo/main.py", line 360, in main_func
bpaired, sfleft_reads, sfright_reads, sfsingle_reads)
File "/data/Bioinfo/bioinfo-proj-bobbie/newProgs/REPdenovo/Assembly.py", line 146, in assembly
with open(sconcate,"r") as fin:
IOError: [Errno 2] No such file or directory: './repdenovo/30mer.temp_contigs.fa'

My config file is like this

MIN_REPEAT_FREQ 10
RANGE_ASM_FREQ_DEC 2
RANGE_ASM_FREQ_GAP 0.8
K_MIN 30
K_MAX 50
K_INC 10
K_DFT 30
READ_LENGTH 250
READ_DEPTH 60
THREADS 60
ASM_NODE_LENGTH_OFFSET -1
MIN_CONTIG_LENGTH 100
IS_DUPLICATE_REPEATS 0.85
COV_DIFF_CUTOFF 0.5
MIN_SUPPORT_PAIRS 20
MIN_FULLY_MAP_RATIO 0.2
TR_SIMILARITY 0.85
JELLYFISH_PATH /usr/local/appl/bio/jellyfish/bin/
VELVET_PATH /usr/local/appl/bio/velvet/bin/
BWA_PATH /usr/local/appl/bio/bwa/bin/
SAMTOOLS_PATH /usr/local/appl/bio/samtools/bin/
REFINER_PATH /data/Bioinfo/bioinfo-proj-bobbie/newProgs/REPdenovo/
CONTIGS_MERGER_PATH /data/Bioinfo/bioinfo-proj-bobbie/newProgs/REPdenovo/
OUTPUT_FOLDER ./repdenovo/
VERBOSE 1

and my raw reads file is like this
[shabanb@melb-compute05 121]$ cat file.txt
/ssd/Prawn_18_R1_val_1.fq 1 550 50
/ssd/Prawn_18_R2_val_2.fq 1 550 50

Thank you for your help,
Bobbie

I'm really interested in testing your software but when I launch the python script I received back the following error message:

python ./main.py -c Assembly -g /home/ubuntu16/tmp/REPdenovo/configuration.txt -r /home/ubuntu16/tmp/REPdenovo/input_reads.txt
Traceback (most recent call last):
File "./main.py", line 405, in
main_func(scommand,sfconfig,sfreads_list)
File "./main.py", line 338, in main_func
read_rawreads_list(sfreads_list)
File "./main.py", line 206, in read_rawreads_list
if parts[0]=="#":##ignore comments
IndexError: list index out of range

configuration and input_reads seems to me OK.
could you help me to fix this issue?

Thanks, alberto

Hi,
when running REPdenovo, the program stops with the following error:
Running command: ./TERefiner_1 -P -b ./test/contigs.fa.itself.sort.bam -r ./test/contigs.fa -o ./test/contigs.fa_no_dup.fa -c 0.9 -g ...
/bin/sh: ./TERefiner_1: cannot execute binary file

when trying to compile the TERefiner_1 tool, I got the following error message:

ld: library not found for -lcrt0.o
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [TERefiner] Error 1

Not sure it is a directly related REPdenovo issue but are you still working on a user-friendly possibility to compile TERefiner_1 and ContigsMerger?

Hi @ReedWarbler,

I am trying to use repdenovo and it crashes on me, always during the assembly step. I already downsized the reads to 20% of the forward reads only and it still happens, so not sure if read no. is the problem here.

Here is my error message:

rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/Asm_’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/.fa’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/*.fastq’: No such file or directory
[bwa_index] Pack FASTA... 0.10 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 1.36 seconds elapse.
[bwa_index] Update BWT... 0.05 sec
[bwa_index] Pack forward-only FASTA... 0.08 sec
[bwa_index] Construct SA from BWT and Occ... 0.83 sec
[main] Version: 0.7.5a-r405
[main] CMD: /usr/bin/bwa index /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa
[main] Real time: 2.556 sec; CPU: 2.432 sec
[M::main_mem] read 26467 sequences (6451911 bp)...
[main] Version: 0.7.5a-r405
[main] CMD: /usr/bin/bwa mem -a /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa
[main] Real time: 6.968 sec; CPU: 6.842 sec
[samopen] SAM header is present: 26467 sequences.
open: No such file or directory
[bam_index_build2] fail to open the BAM file.
Index file not found, now create it!!!
Index file cannot be created!!!
Bamtools ERROR: could not open input BAM file: /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa.itself.sort.bam
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa.itself.bam’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa.itself.bam’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa.itself.bam’: No such file or directory
Segmentation fault (core dumped)
Segmentation fault (core dumped)
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.00 sec
[main] Version: 0.7.5a-r405
[main] CMD: /usr/bin/bwa index /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa
[main] Real time: 0.007 sec; CPU: 0.004 sec
[main] Version: 0.7.5a-r405
[main] CMD: /usr/bin/bwa mem -a /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa
[main] Real time: 0.002 sec; CPU: 0.002 sec
[samopen] no @sq lines in the header.
[sam_read1] missing header? Abort!
[bam_header_read] EOF marker is absent. The input is probably truncated.
open: No such file or directory
[bam_index_build2] fail to open the BAM file.
Index file not found, now create it!!!
Index file cannot be created!!!
Bamtools ERROR: could not open input BAM file: /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.itself.bam’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.itself.bam’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.itself.bam’: No such file or directory
open: No such file or directory
[_razf_open] fail to open /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
[fai_build] fail to open the FASTA file /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
open: No such file or directory
[_razf_open] fail to open /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
[fai_build] fail to open the FASTA file /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
[bwa_index] fail to open file '/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa' : No such file or directory
[E::bwa_idx_load] fail to locate the index files
[samopen] no @sq lines in the header.
[sam_read1] missing header? Abort!
[bam_header_read] EOF marker is absent. The input is probably truncated.
open: No such file or directory
[bam_index_build2] fail to open the BAM file.
Index file not found, now create it!!!
Index file cannot be created!!!
Bamtools ERROR: could not open input BAM file: /home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.sa’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.pac’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.bwt’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.ann’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.amb’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.bam’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.bam’: No such file or directory
rm: cannot remove ‘/home/pbrand/repdenovo/med-PA/cutoff_100/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.bam’: No such file or directory
Traceback (most recent call last):
File "/home/pbrand/bin/REPdenovo-master/main.py", line 408, in
main_func(scommand,sfconfig,sfreads_list)
File "/home/pbrand/bin/REPdenovo-master/main.py", line 371, in main_func
RM_DUP_BF_MERGE_CUTOFF, RM_DUP_AF_MERGE_CUTOFF)
File "/home/pbrand/bin/REPdenovo-master/MergeContigs.py", line 91, in merge_contigs
os.rename(foutput,fout_folder+"contigs.fa")
OSError: [Errno 2] No such file or directory

Any idea what's going wrong here?

Best,
Philipp

Hi @ReedWarbler

i'm testing REPdenovo but i do not undersand my ouputs
here the output error :
output_error.txt
my configuration file:
config_file.txt
the read_file:
read_file.txt

and the three output_files wich 2 are empty:
-reads_coverage.txt

dumped_30mers.txt

contigs.fa.txt

Best

Hi and thanks for the great software!

I've been asked to install it, and I like to install all bioinformatics software with bioconda. It will need a typical LICENSE file included in the github repo for me to add it. Is this possible?

Thanks!

Hi!

This issue appears to have some similarities to another open issue (#11) entitled TERefiner_1 error.

I ran REPdenovo and produced a contigs.fa file. I found no obvious errors or warning messages. But I cannot locate an output that contains the repeat coverage information (i.e., X_contig_pairs_info.txt_cov_info_with_cutoff.txt is missing). Below, I tried to describe my analysis in some details, hoping this helps to understand my problem better.

Can I trust the contents of the contigs.fa file or if I should consider that the analysis failed because of the missing output file? Also, if the analysis failed, is it possible to tell what was the error so I can try to fix it?

Thanks!

Modules

I ran REPdenovo on a machine with Red Hat Enterprise Linux 7.5 (24 cores, 1.5T of memory). These were the modules I had available at the time I executed REPdenovo:

Currently Loaded Modulefiles:
  1) pymods/2.7.5      3) samtools/1.3.1    5) jellyfish/2.2.6   7) repdenovo/0.0
  2) perlmods/5.16.3   4) bamtools/2.4.1    6) velvet/1.2.10     8) bwa/0.7.17

Input Files

paired_reads.txt

/projects/asterias/00_originalData/eAstRub1_27786_7#1_R1.fastq.gz 1 450 50
/projects/asterias/00_originalData/eAstRub1_27786_7#1_R2.fastq.gz 1 450 50

config.txt

MIN_REPEAT_FREQ 10
RANGE_ASM_FREQ_DEC 2
RANGE_ASM_FREQ_GAP 0.8
K_MIN 23
K_MAX 49
K_INC 2
READ_LENGTH 151
GENOME_LENGTH 586800000
MIN_CONTIG_LENGTH 150
ASM_NODE_LENGTH_OFFSET -1
IS_DUPLICATE_REPEATS 0.85
COV_DIFF_CUTOFF 0.5
MIN_SUPPORT_PAIRS 20
MIN_FULLY_MAP_RATIO 0.2
TR_SIMILARITY 0.85
TREADS 24
BWA_PATH /apps/pkg/bwa/0.7.17/rhel7_u5/gnu/bin/bwa
SAMTOOLS_PATH /apps/pkg/bwa/0.7.17/rhel7_u5/gnu/bin/samtools
JELLYFISH_PATH /apps/pkg/jellyfish-2.2.6/rhel7_u2-x86_64/gnu/bin/
VELVET_PATH /apps/pkg/velvet-1.2.10/bin/
REFINER_PATH /apps/pkg/repdenovo-0.0/TERefiner_1
CONTIGS_MERGER_PATH /apps/pkg/repdenovo-0.0/ContigsMerger
OUTPUT_FOLDER /nobackup/asterias/20200115_repdenovo
VERBOSE 1

Template command line for assembly

main.py -c Assembly -g ${CONFI} -r ${INPUT}

Template command line for scaffolding

main.py -c Scaffolding -g ${CONFI} -r ${INPUT}

Output files

Alignments

Several large SAM and BAM files were created.

Contigs

The file contigs.fa occupies 12M of disk space and contains 11,939,015 nucleotides accross 6,721 contigs.

Files with 'info' on their names

Several files named similarly to X_contig_pairs_info.txt_cov_info_with_cutoff.txt were created, most of them are empty.

0	0_contig_pairs_info.txt_discarded.txt
0	0_contig_pairs_info.txt_merged.txt
0	0_contig_pairs_info.txt_temp_ContigsConnections.txt
12M	contigs.fa_no_dup.fa.merge.info

Standard error and standard output

See crompressed file std.tar.gz, attached here.
std.tar.gz

I tried running the assembly portion and got an error that it doesn't recognize an option set in Jellyfish. This isn't something I designate so not really sure how to address. Any ideas?

/REPdenovo$ python ./main.py -c Assembly -g configFileFUK.txt -r Fuk_raw_reads.txt
Calculating average coverage....
Running command: Running command: echo $(wc -l /TowerData/home/colleen/Fukomys_reads/SRR960036_1.fastq)... ...
Running command: The number of reads in file /TowerData/home/colleen/Fukomys_reads/SRR960036_1.fastq is ('631034320 /TowerData/home/colleen/Fukomys_reads/SRR960036_1.fastq\n', None) ...
Running command: Running command: echo $(wc -l /TowerData/home/colleen/Fukomys_reads/SRR960036_2.fastq)... ...
Running command: The number of reads in file /TowerData/home/colleen/Fukomys_reads/SRR960036_2.fastq is ('631034320 /TowerData/home/colleen/Fukomys_reads/SRR960036_2.fastq\n', None) ...
Read coverage is: 18.0763463998
rm: cannot remove ‘./FukomysTE/Asm_’: No such file or directory
rm -r ./FukomysTE/Asm_
rm: cannot remove ‘./FukomysTE/.fa’: No such file or directory
rm ./FukomysTE/.fa
rm: cannot remove ‘./FukomysTE/.fastq’: No such file or directory
rm ./FukomysTE/.fastq
Working on 30mer now...
Counting kmers...
Running command: /usr/local/bin/jellyfish count -s 500M --bf-size 30M -C -m 30 -t 15 -o ./FukomysTE/mer_counts.jf -F 2 /TowerData/home/colleen/Fukomys_reads/SRR960036_1.fastq /TowerData/home/colleen/Fukomys_reads/SRR960036_2.fastq...
count: unrecognized option '--bf-size'
Use --usage or --help for some help
Running command: /usr/local/bin/jellyfish dump -L 180 -o ./FukomysTE/dumped_30mers.txt ./FukomysTE/mer_counts.jf...
terminate called after throwing an instance of 'jellyfish::compacted_hash::ErrorReading'
what(): './FukomysTE/mer_counts.jf': File truncated
Aborted (core dumped)
Highest 30mer frequency is 0
Traceback (most recent call last):
File "./main.py", line 408, in
main_func(scommand,sfconfig,sfreads_list)
File "./main.py", line 369, in main_func
bpaired, sfleft_reads, sfright_reads, sfsingle_reads)
File "/TowerData/home/colleen/REPdenovo/Assembly.py", line 146, in assembly
with open(sconcate,"r") as fin:
IOError: [Errno 2] No such file or directory: './FukomysTE/30mer.temp_contigs.fa'

It seems REPdenovo requires Python2 and does not run on python3. However python2 is end-of-life (https://pythonclock.org/ ). Are there any plans to have REPdenovo run on python 3 ?

Hi,

When I run contigsMerger I get the following error
[shabanb@melb-compute05 121]$ /data/Bioinfo/bioinfo-proj-bobbie/newProgs/REPdenovo/ContigsMerger-v0.1.9/ContigsMerger
Arrange error! 0 6

While running within the program, the following command doesn't produce any output

/data/Bioinfo/bioinfo-proj-bobbie/newProgs/REPdenovo/ContigsMerger-v0.1.9/ContigsMerger -s 0.2 -i1 -6.0 -i2 -6.0 -x 15 -k 10 -t 15 -m 1 -o ./repOut22/contigs.fa_no_dup.fa.merge.info ./repOut22/contigs.fa_no_dup.fa > ./repOut22/contigs.fa_no_dup.fa.merged.fa

The software continues on but fails when it tries to create a bam file

Running command: Running command: samtools faidx ./repOut22/contigs.fa_no_dup.fa.merged.fa ...
[bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 303: Success
[E::bwa_idx_load_from_disk] fail to locate the index files
[samopen] no @sq lines in the header.
[sam_read1] missing header? Abort!
[bam_header_read] EOF marker is absent. The input is probably truncated.
open: No such file or directory
[bam_index_build2] fail to open the BAM file.
Running command: /data/Bioinfo/bioinfo-proj-bobbie/newProgs/REPdenovo/TERefiner_1 -P -b ./repOut22/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r ./repOut22/contigs.fa_no_dup.fa.merged.fa -o ./repOut22/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.85 ...
Index file not found, now create it!!!
Index file cannot be created!!!
Bamtools ERROR: could not open input BAM file: ./repOut22/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam

I'm thinking because the ontigs.fa_no_dup.fa.merged.fa.no_dup.fa is empty.

Is there a way to overcome this? I have the original_contigs_before_merging.fa file, which is 27Mb in size.

any help would be greatly appreciated,

thankyou,
bobbie

This is a report of issues with the variable ending in "_PATH" on the configuration file (with a fix).

The configuration file for REPdenovo's main.py take several paths to different applications and directories (BWA_PATH, SAMTOOLS_PATH,
JELLYFISH_PATH, VELVET_PATH, REFINER_PATH,
CONTIGS_MERGER_PATH, and OUTPUT_FOLDER). I had multiple issues setting incomplete paths or using the GLOBAL option for some of them. The best approach seems to be giving complete paths to each of those variables. However, the fact that some have to point to specific files (BWA_PATH, SAMTOOLS_PATH, REFINER_PATH, and CONTIGS_MERGER_PATH) while the others have to point towards directories is confusing.

I am reporting this as an issue because it's not well described on the program's documentation and I hope it might help other users. The fix is simple, simply add the file when setting BWA_PATH, SAMTOOLS_PATH, REFINER_PATH, and CONTIGS_MERGER_PATH but leave other paths pointing just to the directories that contain the files of interest. I suggest adding a comment on the program's documentation and perhaps make these variables follow the same pattern (pointing towards directories, not files) on future versions.

Here is a template for the configuration file when no variables are set to GLOBAL:

MIN_REPEAT_FREQ 10
RANGE_ASM_FREQ_DEC 2
RANGE_ASM_FREQ_GAP 0.8
K_MIN 30
K_MAX 50
K_INC 10
K_DFT 30
READ_LENGTH 250
GENOME_LENGTH 1956000000
MIN_CONTIG_LENGTH 249
ASM_NODE_LENGTH_OFFSET -1
IS_DUPLICATE_REPEATS 0.85
COV_DIFF_CUTOFF 0.5
MIN_SUPPORT_PAIRS 20
MIN_FULLY_MAP_RATIO 0.2
TR_SIMILARITY 0.85
TREADS 8
BWA_PATH /my/home/bwa-0.7.17/gnu/bwa
SAMTOOLS_PATH /my/home/samtools/1.3.1/bin/samtools
JELLYFISH_PATH /my/home/jellyfish-2.2.6/bin/
VELVET_PATH /my/home/velvet-1.2.10/bin/
REFINER_PATH /my/home/repdenovo-0.0/TERefiner_1
CONTIGS_MERGER_PATH /my/home/repdenovo-0.0/ContigsMerger
OUTPUT_FOLDER /my/home/output_dir
VERBOSE 1

Hi Chong,

I'am from France and I think I have some problems with TERefiner_1. I wanted to know is it important for the rest of my analyzes? I obtain my contigs.fa but after Scaffolding I have zero informations in my X_contig_pairs_info.txt_cov_info_with_cutoff.txt .

Running command: /usr/local/src/REPdenovo/TERefiner_1 -P -b ./Siek14_Repeatelm_12X/contigs.fa.itself.sort.bam -r ./Siek14_Repeatelm_12X/contigs.fa -o ./Siek14_Repeatelm_12X/contigs.fa_n o_dup.fa -c 0.9 -g ... rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa.itself.bam': Aucun fichier ou dossier de ce type rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa.itself.bam': Aucun fichier ou dossier de ce type rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa.itself.bam': Aucun fichier ou dossier de ce type Running command: /usr/local/src/REPdenovo/ContigsMerger -s 0.2 -i1 -6.0 -i2 -6.0 -x 15 -y 50 -k 10 -t 15 -m 1 -o ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merge.info ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa > ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa ... Running command: Running command: samtools faidx ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa ... [bwa_index] Pack FASTA... 0.12 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 5.07 seconds elapse. [bwa_index] Update BWT... 0.09 sec [bwa_index] Pack forward-only FASTA... 0.07 sec [bwa_index] Construct SA from BWT and Occ... 2.19 sec [main] Version: 0.7.15-r1140 [main] CMD: bwa index ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa [main] Real time: 8.361 sec; CPU: 7.540 sec [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 4034 sequences (10001826 bp)... [M::process] read 5595 sequences (6324459 bp)... [M::mem_process_seqs] Processed 4034 reads in 71.228 CPU sec, 71.386 real sec [M::mem_process_seqs] Processed 5595 reads in 46.156 CPU sec, 46.256 real sec [main] Version: 0.7.15-r1140 [main] CMD: bwa mem -a ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa [main] Real time: 117.819 sec; CPU: 117.456 sec Running command: /usr/local/src/REPdenovo/TERefiner_1 -P -b ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.itself.sort.bam -r ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa -o ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -c 0.85 -g ... rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.itself.bam': Aucun fichier ou dossier de ce type rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.itself.bam': Aucun fichier ou dossier de ce type rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.itself.bam': Aucun fichier ou dossier de ce type Running command: Running command: samtools faidx ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa ... [bwa_index] Pack FASTA... 0.08 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 2.97 seconds elapse. [bwa_index] Update BWT... 0.06 sec [bwa_index] Pack forward-only FASTA... 0.05 sec [bwa_index] Construct SA from BWT and Occ... 1.39 sec [main] Version: 0.7.15-r1140 [main] CMD: bwa index ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa [main] Real time: 5.104 sec; CPU: 4.552 sec [M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 4162 sequences (10002529 bp)...
[M::process] read 1173 sequences (877888 bp)...
[M::mem_process_seqs] Processed 4162 reads in 64.264 CPU sec, 64.418 real sec
[M::mem_process_seqs] Processed 1173 reads in 7.060 CPU sec, 7.065 real sec
[main] Version: 0.7.15-r1140
[main] CMD: bwa mem -a ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa
[main] Real time: 71.635 sec; CPU: 71.368 sec
Running command: /usr/local/src/REPdenovo/TERefiner_1 -P -b ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.sort.bam -r ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa -o ./Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.no_contained.fa -c 0.85 ...
rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.bam': Aucun fichier ou dossier de ce type
rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.bam': Aucun fichier ou dossier de ce type
rm: impossible de supprimer './Siek14_Repeatelm_12X/contigs.fa_no_dup.fa.merged.fa.no_dup.fa.itself.bam': Aucun fichier ou dossier de ce type

It's very emergency because I need to finish my intenrship, Thank you so much !

I find TERefiner cannot work, so I build that manually.

cd TERefiner && make && cd ..

Then it uses bamtools-master in the process, so I download bamtools, rename it, build it and put it in the REPdenovo folder.

Then another issues happen:

g++ -O3 -Wall -static -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -o TERefiner_1 public_func.o StrOperation.o local_alignment.o Alignment.o bam_parse.o fai_parser.o contigs.o Coverage.o scaffolding.o RepeatsClassifier.o refiner.o main.o
-lbamtools -lz -lm
/usr/bin/ld: cannot find -lstdc++
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc

how to solve that?

cd TERefiner && make && cd .. = after this command fatal error api/BamReader.h: No such file or directory compilation terminated is generating.

g++ -O3 -Wall -static -I../bamtools/build/src/api/include -I../bamtools/build/src/include -L -Wl,-rpath, -c bam_parse.cpp
In file included from bam_parse.cpp:1:0:
bam_parse.h:4:27: fatal error: api/BamReader.h: No such file or directory
compilation terminated.
Makefile:19: recipe for target 'bam_parse.o' failed
make: *** [bam_parse.o] Error 1

I even tried multiple links from bamtools repository and build folder to REPdenovo/bamtools-master, and the file is never found.
kindly, solve as i have to finish my project within 10 days.