allHIC_partition crashes

[Karina-atriztan]

Hi I´m trying to solve the chromosomes of a fungal specie (haploid). I successfully ran the correction steps. When I try to run the partition step, I have an error indicating that I have only 34 RE for MboI.

My command is: ALLHiC_partition -r seq.HiCcorrected.fasta -e GATC -k 1 -b sample. unique.REduced.paired_only.bam

and the full error is: Extract function: calculate an empirical distribution of Hi-C link size based on intra-contig links CMD: allhic extract sample.unique.REduced.paired_only.bam seq.HiCcorrected.fasta --RE GATC 23:35:14 writeRE | NOTICE RE counts in 34 contigs (total: 34, avg 1 per 1063659 bp) written to sample.unique.REduced.paired_only.counts_GATC.txt 23:35:14 extractContigLinks | NOTICE Parse bamfile sample.unique.REduced.paired_only.bam 23:35:14 extractContigLinks | ERROR Cannot open bamfile sample.unique.REduced.paired_only.bam (sam: malformed header line: line 36: "@HD\tVN:1.5\tSO:unsorted\tGO:query") Partition contigs based on prunning bam file CMD: allhic partition sample.unique.REduced.paired_only.counts_GATC.txt sample.unique.REduced.paired_only.pairs.txt 1 --minREs 25 23:35:14 ReadCSVLines | NOTICE Parse csvfile sample.unique.REduced.paired_only.counts_GATC.txt 23:35:14 readRE | NOTICE Loaded 34 contig RE lengths for normalization from sample.unique.REduced.paired_only.counts_GATC.txt 23:35:14 skipContigsWithFewREs | NOTICE skipContigsWithFewREs with MinREs = 25 (RE = only.counts) Contig #0 (contig_1_1_2003999) has 1 RE sites -> MARKED SHORT Contig #1 (contig_1_2004000_2004999) has 1 RE sites -> MARKED SHORT Contig #2 (contig_1_2005000_5057999) has 1 RE sites -> MARKED SHORT Contig #3 (contig_1_5058000_5059999) has 1 RE sites -> MARKED SHORT Contig #4 (contig_1_5059999_6640822) has 1 RE sites -> MARKED SHORT Contig #5 (contig_10_1_405999) has 1 RE sites -> MARKED SHORT Contig #6 (contig_10_406000_406999) has 1 RE sites -> MARKED SHORT Contig #7 (contig_10_407000_1245999) has 1 RE sites -> MARKED SHORT Contig #8 (contig_10_1246000_1246999) has 1 RE sites -> MARKED SHORT Contig #9 (contig_10_1246999_1417455) has 1 RE sites -> MARKED SHORT Contig #10 (contig_11) has 1 RE sites -> MARKED SHORT Contig #11 (contig_12) has 1 RE sites -> MARKED SHORT Contig #12 (contig_2_1_484999) has 1 RE sites -> MARKED SHORT Contig #13 (contig_2_485000_488999) has 1 RE sites -> MARKED SHORT Contig #14 (contig_2_489000_2387999) has 1 RE sites -> MARKED SHORT Contig #15 (contig_2_2388000_2388999) has 1 RE sites -> MARKED SHORT Contig #16 (contig_2_2388999_6512223) has 1 RE sites -> MARKED SHORT Contig #17 (contig_3) has 1 RE sites -> MARKED SHORT Contig #18 (contig_4_1_2127999) has 1 RE sites -> MARKED SHORT Contig #19 (contig_4_2128000_2128999) has 1 RE sites -> MARKED SHORT Contig #20 (contig_4_2128999_4255974) has 1 RE sites -> MARKED SHORT Contig #21 (contig_5_1_1483999) has 1 RE sites -> MARKED SHORT Contig #22 (contig_5_1484000_1484999) has 1 RE sites -> MARKED SHORT Contig #23 (contig_5_1484999_3064596) has 1 RE sites -> MARKED SHORT Contig #24 (contig_6) has 1 RE sites -> MARKED SHORT Contig #25 (contig_7_1_1162999) has 1 RE sites -> MARKED SHORT Contig #26 (contig_7_1163000_1163999) has 1 RE sites -> MARKED SHORT Contig #27 (contig_7_1163999_2073182) has 1 RE sites -> MARKED SHORT Contig #28 (contig_8_1_1647999) has 1 RE sites -> MARKED SHORT Contig #29 (contig_8_1648000_1648999) has 1 RE sites -> MARKED SHORT Contig #30 (contig_8_1649000_1676999) has 1 RE sites -> MARKED SHORT Contig #31 (contig_8_1677000_1677999) has 1 RE sites -> MARKED SHORT Contig #32 (contig_8_1677999_1978163) has 1 RE sites -> MARKED SHORT Contig #33 (contig_9) has 1 RE sites -> MARKED SHORT 23:35:14 skipContigsWithFewREs | NOTICE Marked 34 contigs (avg 1.0 RE sites, len 1063659) since they contain too few REs (MinREs = 25) 23:35:14 ReadCSVLines | NOTICE Parse csvfile sample.unique.REduced.paired_only.pairs.txt 23:35:14 mustOpen | CRITIC open sample.unique.REduced.paired_only.pairs.txt: no such file or directory

Can you please help me to solve this error.