MetaWrap got stuck at sorting the alignment stage #579
Description
Dear developer
I'm using the binning module for making bins from assembly files created using long reads by Canu, Flye, and MDBG. The assembly sizes for Canu, Flye, and MDBG are approximately 178 MB, 304 MB, and 504 MB, respectively. The read file is approximately 11 GB (not compressed).
MetaWrap finished the binning for Canu in a reasonable time (around 30 min), but got stuck for both Flye and MDBG without an error, yet for almost 1 day. Below is the terminal output for MDBG; it is stuck at the same stage for Flye as well.
(metawrap-env) [user@biolab ~]$ /data2/user_Remote/HiAS/For_Gh/metawrap_single_read_MDBG.sh
[Fri Sep 19 13:48:59 CEST 2025] Running metaWRAP binning for Zone01 ...
metawrap binning --single-end --metabat1 --metabat2 --maxbin2 --concoct -t 55 -m 500 -a /data2/user_Remote/HiAS/For_Gh/Nanopore_assemblies/MDBG/Zone01.fasta -o /data2/user_Remote/HiAS/For_Gh/MetaWrap_MDBG/Zone01 /data2/user_Remote/HiAS/user_HiAS/0_Fq_Nanopore/zone/Zone01.fastq
----- Entered read type: single -----
########################################################################################################################
ALIGNING READS TO MAKE COVERAGE FILES
########################################################################################################################
Warning: /data2/user_Remote/HiAS/For_Gh/MetaWrap_MDBG/Zone01 already exists.
rm: cannot remove '/data2/user_Remote/HiAS/For_Gh/MetaWrap_MDBG/Zone01/*checkm': No such file or directory
----- making copy of assembly file -----
----- /data2/user_Remote/HiAS/For_Gh/Nanopore_assemblies/MDBG/Zone01.fasta -----
----- Indexing assembly file -----
[bwa_index] Pack FASTA... 3.68 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=1048935532, availableWord=85806540
[BWTIncConstructFromPacked] 10 iterations done. 99999996 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999996 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 299999996 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 399541772 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 490796428 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 571899804 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 643980668 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 708042348 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 764976492 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 815575708 characters processed.
[BWTIncConstructFromPacked] 110 iterations done. 860544380 characters processed.
[BWTIncConstructFromPacked] 120 iterations done. 900508620 characters processed.
[BWTIncConstructFromPacked] 130 iterations done. 936024924 characters processed.
[BWTIncConstructFromPacked] 140 iterations done. 967587852 characters processed.
[BWTIncConstructFromPacked] 150 iterations done. 995637036 characters processed.
[BWTIncConstructFromPacked] 160 iterations done. 1020563212 characters processed.
[BWTIncConstructFromPacked] 170 iterations done. 1042713644 characters processed.
[bwt_gen] Finished constructing BWT in 174 iterations.
[bwa_index] 348.43 seconds elapse.
[bwa_index] Update BWT... 2.35 sec
[bwa_index] Pack forward-only FASTA... 2.02 sec
[bwa_index] Construct SA from BWT and Occ... 134.92 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /data2/user_Remote/HiAS/For_Gh/MetaWrap_MDBG/Zone01/work_files/assembly.fa
[main] Real time: 516.635 sec; CPU: 491.401 sec
----- Aligning /data2/user_Remote/HiAS/user_HiAS/0_Fq_Nanopore/zone/Zone01.fastq back to -----
----- assembly, and sorting the alignment -----
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 270652 sequences (550000745 bp)...
[M::process] read 277304 sequences (550001543 bp)...
[M::mem_process_seqs] Processed 270652 reads in 2503.560 CPU sec, 48.331 real sec
[M::process] read 261246 sequences (550006088 bp)...
[M::mem_process_seqs] Processed 277304 reads in 2765.550 CPU sec, 204.619 real sec
[M::process] read 251064 sequences (550003224 bp)...
[M::mem_process_seqs] Processed 261246 reads in 2552.908 CPU sec, 48.593 real sec
[M::process] read 249288 sequences (550005347 bp)...
[M::mem_process_seqs] Processed 251064 reads in 2630.868 CPU sec, 53.041 real sec
[M::process] read 253034 sequences (550001074 bp)...
[M::mem_process_seqs] Processed 249288 reads in 2638.626 CPU sec, 60.362 real sec
[M::process] read 254216 sequences (550004350 bp)...
[M::mem_process_seqs] Processed 253034 reads in 2603.445 CPU sec, 50.986 real sec
[M::process] read 252808 sequences (550002427 bp)...
[M::mem_process_seqs] Processed 254216 reads in 2743.425 CPU sec, 95.383 real sec
[M::process] read 247330 sequences (550001334 bp)...
[M::mem_process_seqs] Processed 252808 reads in 2698.823 CPU sec, 152.175 real sec
[M::process] read 237192 sequences (550001496 bp)...
[M::mem_process_seqs] Processed 247330 reads in 10867.836 CPU sec, 8265.008 real sec
[M::process] read 138094 sequences (319805285 bp)...
THanks for your help