zsh: killed

[ericgmoreno]

Hi!

I am trying to assemble a mitochondrial genome from freshwater crabs in my Laptop and on the rounds part the process fails. I already assembled two mitogenomes a few months ago and it worked fine. I have no idea why this is happening now, I even reinstalled the pipeline but it still doesn't work. In other hand, I had issues to run the libraries during the reinstalling.

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python get_organelle_from_reads.py -1 R1_4M_P.fastq.gz -2 R2_4M_P.fastq.gz -R 10 -k 21,45,65,85,105 -F animal_mt -o TP_4M_mt_out

GetOrganelle v1.7.6.1

get_organelle_from_reads.py assembles organelle genomes from genome skimming data. Find updates in https://github.com/Kinggerm/GetOrganelle and see README.md for more information.

Python 3.8.3 (default, Jul 2 2020, 11:26:31) [Clang 10.0.0 ] PLATFORM: Darwin MacBook-Air-de-PepeLuis.local 21.6.0 Darwin Kernel Version 21.6.0: Thu Sep 29 20:12:57 PDT 2022; root:xnu-8020.240.7~1/RELEASE_X86_64 x86_64 i386 PYTHON LIBS: GetOrganelleLib 1.7.6.1; numpy 1.18.5; sympy 1.6.1; scipy 1.5.0; psutil 5.7.0 DEPENDENCIES: Bowtie2 2.4.1; SPAdes 3.14.0; Blast 2.9.0 GETORG_PATH=/Users/pepeluis/.GetOrganelle SEED DB: animal_mt 0.0.0 LABEL DB: animal_mt 0.0.1 WORKING DIR: /Users/pepeluis/Documents/Doctorado_Eric/GetOrganelle-1.7.6.1 get_organelle_from_reads.py -1 R1_4M_P.fastq.gz -2 R2_4M_P.fastq.gz -R 10 -k 21,45,65,85,105 -F animal_mt -o TP_4M_mt_out

2022-11-22 21:32:03,695 - INFO: Pre-reading fastq ... 2022-11-22 21:32:03,696 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf') 2022-11-22 21:32:03,830 - INFO: Tasting 100000+100000 reads ... 2022-11-22 21:32:27,179 - INFO: Tasting 500000+500000 reads ... 2022-11-22 21:33:42,627 - INFO: Estimating reads to use finished. 2022-11-22 21:33:42,627 - INFO: Unzipping reads file: R1_4M_P.fastq.gz (196007060 bytes) 2022-11-22 21:33:46,376 - INFO: Unzipping reads file: R2_4M_P.fastq.gz (218846862 bytes) 2022-11-22 21:33:50,465 - INFO: Counting read qualities ... 2022-11-22 21:33:50,651 - INFO: Identified quality encoding format = Sanger 2022-11-22 21:33:50,651 - INFO: Phred offset = 33 2022-11-22 21:33:50,653 - INFO: Trimming bases with qualities (0.00%): 33..33 ! 2022-11-22 21:33:50,755 - INFO: Mean error rate = 0.0025 2022-11-22 21:33:50,756 - INFO: Counting read lengths ... 2022-11-22 21:33:57,228 - INFO: Mean = 142.4 bp, maximum = 151 bp. 2022-11-22 21:33:57,228 - INFO: Reads used = 1981613+1981613 2022-11-22 21:33:57,229 - INFO: Pre-reading fastq finished.

2022-11-22 21:33:57,229 - INFO: Making seed reads ... 2022-11-22 21:33:57,229 - INFO: Seed bowtie2 index existed! 2022-11-22 21:33:57,229 - INFO: Mapping reads to seed bowtie2 index ... 2022-11-22 21:36:20,856 - INFO: Mapping finished. 2022-11-22 21:36:20,857 - INFO: Seed reads made: TP_4M_mt_out/seed/animal_mt.initial.fq (471248 bytes) 2022-11-22 21:36:20,858 - INFO: Making seed reads finished.

2022-11-22 21:36:20,858 - INFO: Checking seed reads and parameters ... 2022-11-22 21:36:20,858 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s). 2022-11-22 21:36:20,859 - INFO: If the result graph is not a circular organelle genome, 2022-11-22 21:36:20,859 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run. 2022-11-22 21:36:23,942 - INFO: Pre-assembling mapped reads ... 2022-11-22 21:36:29,958 - INFO: Pre-assembling mapped reads finished. 2022-11-22 21:36:29,959 - INFO: Estimated animal_mt-hitting base-coverage = 17.37 2022-11-22 21:36:30,206 - WARNING: Guessing that you are using too few data for assembling animal_mt! 2022-11-22 21:36:30,206 - WARNING: GetOrganelle is still trying ... 2022-11-22 21:36:30,206 - INFO: Estimated word size(s): 41 2022-11-22 21:36:30,206 - INFO: Setting '-w 41' 2022-11-22 21:36:30,207 - INFO: Setting '--max-extending-len inf' 2022-11-22 21:36:30,305 - INFO: Checking seed reads and parameters finished.

2022-11-22 21:36:30,306 - INFO: Making read index ... 2022-11-22 21:37:09,900 - INFO: Mem 1.694 G, 3474249 candidates in all 3963226 reads 2022-11-22 21:37:09,900 - INFO: Pre-grouping reads ... 2022-11-22 21:37:09,900 - INFO: Setting '--pre-w 41' 2022-11-22 21:37:10,516 - INFO: Mem 1.554 G, 200000/337685 used/duplicated 2022-11-22 21:37:36,921 - INFO: Mem 3.266 G, 4380 groups made. 2022-11-22 21:37:37,315 - INFO: Making read index finished.

2022-11-22 21:37:37,315 - INFO: Extending ... 2022-11-22 21:37:37,315 - INFO: Adding initial words ... 2022-11-22 21:37:37,408 - INFO: AW 75352 2022-11-22 21:51:52,431 - INFO: Round 1: 3474249/3474249 AI 2224493 AW 86979046 Mem 1.053 zsh: killed python get_organelle_from_reads.py -1 R1_4M_P.fastq.gz -2 R2_4M_P.fastq.gz -R