problem with digested reads

[mmarbout]

hicstuff seems to have a serious problem when using the whole pipeline with a lot of predigested reads. The pipeline has aligned the for reads but then do not align the reverse reads even if the software appears to be still running. the log files is ok.

hicstuff: v3.2.2 log file

date: 2024-07-15 18:18:46

enzyme: DpnII,HinfI

input1: /pasteur/zeus/projets/p02/rsg_fast/mmarbout/projets/B2CH/260_dig_R1.fq.gz

input2: /pasteur/zeus/projets/p02/rsg_fast/mmarbout/projets/B2CH/260_dig_R2.fq.gz

ref: /pasteur/zeus/projets/p02/rsg_fast/mmarbout/projets/B2CH/Contact_Map/aminovorans_V3//index/amino

---

2024-07-15,18:18:46 :: INFO :: The default output format is now .cool. The Hi-C matrix will be generated with cooler v0.9.3 (Abdennur & Mirny, Bioinformatics 2020).
2024-07-15,18:18:47 :: INFO :: Checking content of fastq files.
2024-07-15,18:25:28 :: INFO :: 143446111 reads found in each fastq file.

the same command used with the undigested reads works perfectly

hicstuff: v3.2.2 log file

date: 2024-07-15 13:20:18

enzyme: DpnII,HinfI

input1: /pasteur/zeus/projets/p02/rsg_fast/mmarbout/projets/B2CH/MM260a_nvq_R1.fq.gz

input2: /pasteur/zeus/projets/p02/rsg_fast/mmarbout/projets/B2CH/MM260a_nvq_R2.fq.gz

ref: /pasteur/zeus/projets/p02/rsg_fast/mmarbout/projets/B2CH/Contact_Map/aminovorans_V2//index/para

---

2024-07-15,13:20:18 :: INFO :: The default output format is now .cool. The Hi-C matrix will be generated with cooler v0.9.3 (Abdennur & Mirny, Bioinformatics 2020).
2024-07-15,13:20:19 :: INFO :: Checking content of fastq files.
2024-07-15,13:25:00 :: INFO :: 72381158 reads found in each fastq file.
2024-07-15,13:48:51 :: INFO :: 2% reads (single ends) mapped with Q >= 30 (2858269/144762316)
2024-07-15,13:50:00 :: INFO :: 1043754 pairs successfully mapped (1.44%)
2024-07-15,13:50:11 :: INFO :: 29% PCR duplicates have been filtered out (303726 / 1043754 pairs)
2024-07-15,13:50:11 :: INFO :: 740028 pairs remaining after removing PCR duplicates
2024-07-15,13:50:12 :: INFO :: Generating matrix from pairs file /pasteur/zeus/projets/p02/rsg_fast/mmarbout/projets/B2CH/Contact_Map/aminovorans_V2//temp/valid_idx_pcrfree.pairs (740028 pairs in the file)
2024-07-15,13:50:25 :: INFO :: Fetching mapping and pairing stats
2024-07-15,13:50:25 :: WARNING :: IndexError. Stats not compiled.
2024-07-15,13:50:29 :: INFO :: Contact map generated after 0h 30m 11s

could you help me with this problem ?