Segmentation fault - not sure how to debug
Opened this issue · 2 comments
elsherbini commented
I ran the following command on an HPC node with 20 cores and 220GB of RAM
./CAMMiQ/cammiq --build --both -k 21 -L 120 -Lmax 60 -f input/input_genomes_manual_derep.map -D temp/07.prepare_cammiq_genomes/ -t 20
Warning: missing parameter h, set to default h = 26.
Prepared species information of every fasta file.
****************************
Total num bases: 314011798
Total num genomes: 69
Total num contigs: 22192
****************************
Input string get prepared.
Time for computing suffix array: 27260 ms.
Time for computing reverse suffix array: 2692 ms.
Time for computing generalized suffix array: 3395 ms.
Time for computing LCP array: 1261 ms.
Deleted temp file gsa.bin.
Time for resetting memory for LCP0 computation: 408 ms.
Time for computing LCP0 array: 1390 ms.
Time for computing OCC array: 195 ms.
Time for computing minimum unique substrings: 575 ms.
/usr/bin/bash: line 1: 21430 Segmentation fault ./CAMMiQ/cammiq --build --both -k 21 -L 120 -Lmax 60 -f input/input_genomes_manual_derep.map -D temp/07.prepare_cammiq_genomes/ -t 20
Are there parameters you would change or would requesting more memory help?
MortenEneberg commented
Hi @elsherbini,
Did you manage to get CAMMiQ to work? I cant get the download script to work and saw that you had a .map file - would it be possible for you to share it? It seems that the google drive link to the indexes presented in the paper is no longer available.. https://drive.google.com/drive/u/0/folders/1iL0pZ3Jb3QS6AOwO_IGLS2ZDFQJEHpn0.
Kind regards,
Morten
elsherbini commented
@MortenEneberg I never got it to work, no, but I can share the map file I used. It was just a tab delimitted file with the genome file name, an id, a tax_id, the organism name, and then any other info you want in subsequent columns. I made this by following the example on https://github.com/algo-cancer/CAMMiQ/blob/master/README.md#how-do-i-construct-the-index
ctv05_draft_genome_aditi_NO_PLASMID_20221004.fasta 1 47770 Lactobacillus_crispatus probiotic
0421_295_1_1_MRS7_S415_genome.fna 2 4770 Lactobacillus_crispatus SGB266
Mitchell_12_29_17_H06_S624_genome.fna 3 4770 Lactobacillus_crispatus SGB266
CM_D10_S844_genome.fna 4 4770 Lactobacillus_crispatus SGB266
CM_D06_S812_genome.fna 5 4770 Lactobacillus_crispatus SGB266
Lactobacillus_crispatus_233_S810_genome.fna 6 4770 Lactobacillus_crispatus SGB266
DZD_CM_10_S778_genome.fna 7 4770 Lactobacillus_crispatus SGB266
DZD_CM_17_S785_genome.fna 8 4770 Lactobacillus_crispatus SGB266
Mitchell_12_29_17_C07_S627_genome.fna 9 4770 Lactobacillus_crispatus SGB266
CM_A06_S809_genome.fna 10 4770 Lactobacillus_crispatus SGB266
DZD_CM_08_S776_genome.fna 11 4770 Lactobacillus_crispatus SGB266
DZD_CM_26_S794_genome.fna 12 4770 Lactobacillus_crispatus SGB266
JKR_P1_05_E01_S677_001_genome.fna 13 4770 Lactobacillus_crispatus SGB266
Mitchell_12_29_17_G07_S631_genome.fna 14 4770 Lactobacillus_crispatus SGB266
DZD_CM_29_S797_genome.fna 15 4770 Lactobacillus_crispatus SGB266
DZD_CM_40_S808_genome.fna 16 4770 Lactobacillus_crispatus SGB266
Mitchell_12_29_17_A05_S609_genome.fna 17 4770 Lactobacillus_crispatus SGB266
CM_G07_S823_genome.fna 18 4770 Lactobacillus_crispatus SGB266
JKR_P1_02_B01_S674_001_genome.fna 19 4770 Lactobacillus_crispatus SGB266
CM_G06_S815_genome.fna 20 4770 Lactobacillus_crispatus SGB266
Mitchell_12_29_17_A06_S617_genome.fna 21 4770 Lactobacillus_crispatus SGB266
0421_295_1_2_MRS3_S780_genome.fna 22 4770 Lactobacillus_crispatus SGB266
0795_578_1_1_MRS6_S818_genome.fna 23 4770 Lactobacillus_crispatus SGB266
CM_C03_S787_genome.fna 24 4770 Lactobacillus_crispatus SGB266
CM_A02_S777_genome.fna 25 4770 Lactobacillus_crispatus SGB266
0422_293_1_1_MRS10_S408_genome.fna 26 4770 Lactobacillus_crispatus SGB266
CM_G02_S783_genome.fna 27 4770 Lactobacillus_crispatus SGB266
Mitchell_12_29_17_H07_S632_genome.fna 28 4770 Lactobacillus_crispatus SGB266
CM_D08_S828_genome.fna 29 4770 Lactobacillus_crispatus SGB266
Mitchell_12_29_17_E07_S629_genome.fna 30 4770 Lactobacillus_crispatus SGB266
CM_E09_S837_genome.fna 31 4770 Lactobacillus_crispatus SGB266
CM2261_MRS3_S774_genome.fna 32 4770 Lactobacillus_crispatus SGB266
CM_H07_S824_genome.fna 33 4770 Lactobacillus_crispatus SGB266
JKR_P1_14_F02_S686_001_genome.fna 34 4770 Lactobacillus_crispatus SGB266
JKR_P1_16_H02_S688_001_genome.fna 35 4770 Lactobacillus_crispatus SGB266
CM_B04_S794_genome.fna 36 4770 Lactobacillus_crispatus SGB266
CM2292_MRS1_S784_genome.fna 37 4770 Lactobacillus_crispatus SGB266
CM_A01_S769_genome.fna 38 4770 Lactobacillus_crispatus SGB266
Mitchell_12_29_17_B07_S626_genome.fna 39 4770 Lactobacillus_crispatus SGB266
0795_578_1_1_MRS1_S862_genome.fna 40 4770 Lactobacillus_crispatus SGB266
CM_C05_S803_genome.fna 41 4770 Lactobacillus_crispatus SGB266
JKR_P1_11_C02_S683_001_genome.fna 42 4770 Lactobacillus_crispatus SGB266
CM_E03_S789_genome.fna 43 4770 Lactobacillus_crispatus SGB266
CM_A07_S817_genome.fna 44 4770 Lactobacillus_crispatus SGB266
CM_B03_S786_genome.fna 45 4770 Lactobacillus_crispatus SGB266
CM_F06_S814_genome.fna 46 4770 Lactobacillus_crispatus SGB266
0872_642_1_1_MRS5_S773_genome.fna 47 4770 Lactobacillus_crispatus SGB266
DZD_CM_18_S786_genome.fna 48 4770 Lactobacillus_crispatus SGB266
CM_A03_S785_genome.fna 49 4770 Lactobacillus_crispatus SGB266
CM_F04_S798_genome.fna 50 4770 Lactobacillus_crispatus SGB266
CM_E08_S829_genome.fna 51 4770 Lactobacillus_crispatus SGB266
JKR_P1_06_F01_S678_001_genome.fna 52 4770 Lactobacillus_crispatus SGB266
CM_E05_S805_genome.fna 53 4770 Lactobacillus_crispatus SGB266
JKR_P1_08_H01_S680_001_genome.fna 54 4770 Lactobacillus_crispatus SGB266
JKR_P1_09_A02_S681_001_genome.fna 55 4770 Lactobacillus_crispatus SGB266
CM_A05_S801_genome.fna 56 4770 Lactobacillus_crispatus SGB266
Mitchell_12_29_17_A08_S633_genome.fna 57 4770 Lactobacillus_crispatus SGB266
JKR_P1_07_G01_S679_001_genome.fna 58 4770 Lactobacillus_crispatus SGB266
0421_295_1_1_MRS12_S851_genome.fna 59 4770 Lactobacillus_crispatus SGB266
CM_D07_S820_genome.fna 60 4770 Lactobacillus_crispatus SGB266
DZD_CM_03_S771_genome.fna 61 4770 Lactobacillus_crispatus SGB266
CM_G03_S791_genome.fna 62 4770 Lactobacillus_crispatus SGB266
Mitchell_12_29_17_C03_S595_genome.fna 63 4770 Lactobacillus_crispatus SGB266
CM_A04_S793_genome.fna 64 4770 Lactobacillus_crispatus SGB266
CM_H06_S816_genome.fna 65 4770 Lactobacillus_crispatus SGB266
0795_578_1_1_MRS5_S810_genome.fna 66 4770 Lactobacillus_crispatus SGB266
JKR_P1_15_G02_S687_001_genome.fna 67 4770 Lactobacillus_crispatus SGB266
0055_051_1_3_MRS12_S787_genome.fna 68 4770 Lactobacillus_crispatus SGB266
Mitchell_12_29_17_B05_S610_genome.fna 69 4770 Lactobacillus_crispatus SGB266