mapleforest
commented
3 years ago This means the lastz failed, probably the HM_all_lastz_mThreads.pl could not find the Lastz program or the nib files in your working directory. Have you run the first two example 1&2 successfully?
Hi everyone, I am using haplomerge2 for spliting a diploid genome. After runging sh ./hm.batchA1, the output directory /path/to/raw.axt/ is empty. I checked two log files. The _A1.initiation.log is correct but the _A1.all_lastz.log is not complete.
1 2 3 ========== Start at Tue Feb 23 18:43:12 CST 2021 4 /data/Liangjunmin/opt/biosoft/HaploMerger2_20180603/bin/HM_all_lastz_mThreads.pl --Species 2429sorted 2429sortedx --noself --threads=30 --identity=80 --targetSize=50000000 --querySize=1 600000000 --Force --Delete 5 6 Set to OVER-WRITING mode! 7 Set to Delete mode! 8 Species included: 2429sorted 2429sortedx 9 checking missing gz-compressed multiple-fasta files ... 10 Every required files seem ok, going on ... 11 12 Check existed raw.axt directory ... 13 checking if 2429sorted.2429sortedx.result/raw.axt is existing ... 14 cleaning the evironment anyway ... 15 Thread number is set to ... 30 ! 16 Target file size is ... 50000000 ! 17 Query file size is ... 1600000000 ! 18 Is_noself status is ... 1 ! 19 --notrivial status is ... 0 ! 20 --radius for notrivial function is ... 5000 ! 21 --unmask for covert lowcase letters to upcase letters ... ! 22 go to lastz all to all step ... 23 24 Finished splitting the target fasta file ... 25 HM_all_lastz_target_3602_00.fa 26 HM_all_lastz_target_3602_01.fa 27 HM_all_lastz_target_3602_02.fa 28 HM_all_lastz_target_3602_03.fa 29 HM_all_lastz_target_3602_04.fa 30 HM_all_lastz_target_3602_05.fa 31 HM_all_lastz_target_3602_06.fa 32 HM_all_lastz_target_3602_07.fa 33 HM_all_lastz_target_3602_08.fa 34 HM_all_lastz_target_3602_09.fa 35 HM_all_lastz_target_3602_10.fa 36 HM_all_lastz_target_3602_11.fa 37 HM_all_lastz_target_3602_12.fa 38 HM_all_lastz_target_3602_13.fa 39 HM_all_lastz_target_3602_14.fa 40 HM_all_lastz_target_3602_15.fa HM_all_lastz_target_3602_15.fa 41 HM_all_lastz_target_3602_16.fa 42 HM_all_lastz_target_3602_17.fa 43 HM_all_lastz_target_3602_18.fa 44 HM_all_lastz_target_3602_19.fa 45 HM_all_lastz_target_3602_20.fa 46 HM_all_lastz_target_3602_21.fa 47 HM_all_lastz_target_3602_22.fa 48 HM_all_lastz_target_3602_23.fa 49 HM_all_lastz_target_3602_24.fa 50 HM_all_lastz_target_3602_25.fa 51 HM_all_lastz_target_3602_26.fa 52 HM_all_lastz_target_3602_27.fa 53 HM_all_lastz_target_3602_28.fa 54 HM_all_lastz_target_3602_29.fa 55 HM_all_lastz_target_3602_30.fa 56 HM_all_lastz_target_3602_31.fa 57 HM_all_lastz_target_3602_32.fa 58 HM_all_lastz_target_3602_33.fa 59 Finished splitting the query fasta file ... 60 HM_all_lastz_query_3602_00.fa 61 HM_all_lastz_query_3602_01.fa
Anybody know where was wrong? I made the scoreMatrix.q based on my genome data and the identity was set with 94..96, Is it the reason? The hybrid rate for my genome is 1.08% Thanks.