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algo-cancer / CAMMiQ

Metagenomics microbial abundance quantification
MIT License
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Segmentation fault - not sure how to debug #6

Open elsherbini opened 1 year ago

elsherbini commented 1 year ago

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 1 year ago

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 1 year ago

@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