eperezv
commented
4 months ago Hi, The issue I reported before is now resolved (I run it again and it didn't fail). However, I'm having another issue:
Judging 2_C1-c2-c3-MEGAHIT.assembly.fa_0.3_maxbin2_genomes.496.fa
Judging 2_C1-c2-c3-MEGAHIT.assembly.fa_0.3_maxbin2_genomes.123.fa
Judging 2_C1-c2-c3-MEGAHIT.assembly.fa_0.3_maxbin2_genomes.488.fa
Judging 2_C1-c2-c3-MEGAHIT.assembly.fa_0.3_maxbin2_genomes.36.fa
Judging 2_C1-c2-c3-MEGAHIT.assembly.fa_0.3_maxbin2_genomes.216.fa
Judging 1_C1-2-3-MHM2.contigs.fa_200_concoct_genomes.8.fa
Re-mapping
Settings:
Output files: "Remapping.fasta.*.bt2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
Remapping.fasta
Warning: Empty fasta file: 'Remapping.fasta'
Warning: All fasta inputs were empty
Total time for call to driver() for forward index: 00:00:00
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/eduardo/miniconda3/envs/BASALT/bin/bowtie2-build-s --wrapper basic-0 Remapping.fasta Remapping.fasta
Mapping ['C1_1.clean2.fq', 'C1_2.clean2.fq']
(ERR): "Remapping.fasta" does not exist or is not a Bowtie 2 index
Exiting now ...
[E::hts_open_format] Failed to open file 1.sam
samtools view: failed to open "1.sam" for reading: No such file or directory
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
Samtools sorting 1.bam failed. Redoing
[E::hts_open_format] Failed to open file 1.bam
samtools sort: can't open "1.bam": No such file or directory
rm: cannot remove '1.sam': No such file or directory
Output depth matrix to Re-mapped_depth.txt
Output matrix to Re-mapped_depth.txt
Opening 1 bams
[E::hts_open] fail to open file '1_sorted.bam'
Consolidating headers
Segmentation fault (core dumped)
Output depth matrix to Re-mapped_depth.txt
Output matrix to Re-mapped_depth.txt
Opening 1 bams
[E::hts_open] fail to open file '1_sorted.bam'
Consolidating headers
Segmentation fault (core dumped)
rm: cannot remove '1_sorted.bam': No such file or directory
rm: cannot remove '*.bt2': No such file or directory
rm: cannot remove '1.bam': No such file or directory
Traceback (most recent call last):
File "/home/eduardo/miniconda3/envs/BASALT/bin/BASALT", line 137, in <module>
BASALT_main_d(assembly_list, datasets, num_threads, lr_list, hifi_list, hic_list, eb_list, ram, continue_mode, functional_module, autobining_parameters, refinement_paramter, max_ctn, min_cpn, pwd, QC_software)
File "/home/eduardo/miniconda3/envs/BASALT/bin/BASALT_main_d.py", line 453, in BASALT_main_d
outlier_remover_main('BestBinset', coverage_matrix_list, datasets, lr_list, hifi_list, assembly_mo_list, pwd, num_threads)
File "/home/eduardo/miniconda3/envs/BASALT/bin/S5_Outlier_remover_DL_11012023.py", line 549, in outlier_remover_main
A=outlier_predictor(depth_TNF_matrix, contigs_depth, bin_contigs, datasets, lr, hifi_list, num_threads, nx)
File "/home/eduardo/miniconda3/envs/BASALT/bin/S5_Outlier_remover_DL_11012023.py", line 394, in outlier_predictor
for line in open('Re-mapped_depth.txt','r'):
FileNotFoundError: [Errno 2] No such file or directory: 'Re-mapped_depth.txt'I would appreciate any help to solve it. Thank you
EMBL-PKU
Hello,
I'm trying BASALT with a subset of my data. It looked to work fine until the step "Comparing bins before and after refining process" that failed with the error in the title.