GetOrganelle v1.7.4.1

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 3.10.3 (main, Mar 18 2022, 15:00:24) [GCC 8.5.0 20210514 (Red Hat 8.5.0-4)]
PLATFORM: Linux kingspeak1 4.18.0-348.20.1.el8_5.x86_64 #1 SMP Thu Mar 10 20:59:28 UTC 2022 x86_64 x86_64
PYTHON LIBS: GetOrganelleLib 1.7.4.1; numpy 1.22.3; sympy 1.10.1; scipy 1.8.0; psutil 5.9.0
DEPENDENCIES: Bowtie2 2.2.9; SPAdes genome assembler 3.15.4; Blast 2.11.0
GETORG_PATH=/uufs/chpc.utah.edu/common/home/u6044365/.GetOrganelle
LABEL DB: animal_mt 0.0.1
WORKING DIR: /uufs/chpc.utah.edu/common/home/gompert-group3/projects/troglo_SPY/scripts/GetOrganelle-1.7.4.1
./get_organelle_from_reads.py -s liniphidae_c1_xs.fasta -1 ../../00_Trimmomatic/Tbolo_111_1_paired.fq.gz -2 ../../00_Trimmomatic/Tbolo_111_2_paired.fq.gz -F animal_mt -o ../../HN00176099_hdd1/mitogenomes/Tbolo_111_mitogenome -R 15 -w 95

2022-12-19 14:30:05,152 - INFO: Pre-reading fastq ...
2022-12-19 14:30:05,152 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf')
2022-12-19 14:30:06,321 - INFO: Tasting 100000+100000 reads ...
2022-12-19 14:30:32,076 - INFO: Estimating reads to use finished.
2022-12-19 14:30:32,077 - INFO: Unzipping reads file: ../../00_Trimmomatic/Tbolo_111_1_paired.fq.gz (9713199256 bytes)
2022-12-19 14:30:35,923 - INFO: Unzipping reads file: ../../00_Trimmomatic/Tbolo_111_2_paired.fq.gz (9997086402 bytes)
2022-12-19 14:30:39,859 - INFO: Counting read qualities ...
2022-12-19 14:30:40,208 - INFO: Identified quality encoding format = Sanger
2022-12-19 14:30:40,208 - INFO: Phred offset = 33
2022-12-19 14:30:40,210 - INFO: Trimming bases with qualities (0.00%): 33..33  !
2022-12-19 14:30:40,274 - INFO: Mean error rate = 0.0031
2022-12-19 14:30:40,275 - INFO: Counting read lengths ...
2022-12-19 14:30:50,244 - INFO: Mean = 141.1 bp, maximum = 151 bp.
2022-12-19 14:30:50,245 - INFO: Reads used = 1807596+1819770
2022-12-19 14:30:50,245 - INFO: Pre-reading fastq finished.

2022-12-19 14:30:50,245 - INFO: Making seed reads ...
2022-12-19 14:30:50,286 - INFO: Making seed - bowtie2 index ...
2022-12-19 14:30:50,672 - INFO: Making seed - bowtie2 index finished.
2022-12-19 14:30:50,673 - INFO: Mapping reads to seed bowtie2 index ...
2022-12-19 14:31:49,944 - INFO: Mapping finished.
2022-12-19 14:31:49,945 - INFO: Seed reads made: ../../HN00176099_hdd1/mitogenomes/Tbolo_111_mitogenome/seed/animal_mt.initial.fq (1862688 bytes)
2022-12-19 14:31:49,945 - INFO: Making seed reads finished.

2022-12-19 14:31:49,945 - INFO: Checking seed reads and parameters ...
2022-12-19 14:31:51,185 - INFO: Estimated animal_mt-hitting base-coverage = 12.27
2022-12-19 14:31:51,625 - INFO: Setting '--max-extending-len inf'
2022-12-19 14:31:51,648 - INFO: Checking seed reads and parameters finished.

2022-12-19 14:31:51,648 - INFO: Making read index ...
2022-12-19 14:32:40,842 - INFO: Mem 1.046 G, 2282523 candidates in all 3627366 reads
2022-12-19 14:32:40,849 - INFO: Pre-grouping reads ...
2022-12-19 14:32:40,849 - INFO: Setting '--pre-w 95'
2022-12-19 14:32:41,253 - INFO: Mem 0.969 G, 129551/129551 used/duplicated
2022-12-19 14:32:56,633 - INFO: Mem 1.668 G, 2040 groups made.
2022-12-19 14:32:56,945 - INFO: Making read index finished.

2022-12-19 14:32:56,945 - INFO: Extending ...
2022-12-19 14:32:56,945 - INFO: Adding initial words ...
2022-12-19 14:32:56,994 - INFO: AW 1514
2022-12-19 14:33:23,025 - INFO: Round 1: 2282523/2282523 AI 51 AW 1734 Mem 1.09
2022-12-19 14:33:48,813 - INFO: Round 2: 2282523/2282523 AI 64 AW 2108 Mem 1.09
2022-12-19 14:34:14,658 - INFO: Round 3: 2282523/2282523 AI 78 AW 2500 Mem 1.09
2022-12-19 14:34:40,538 - INFO: Round 4: 2282523/2282523 AI 97 AW 2840 Mem 1.09
2022-12-19 14:35:06,262 - INFO: Round 5: 2282523/2282523 AI 99 AW 2840 Mem 1.09
2022-12-19 14:35:06,262 - INFO: No more reads found and terminated ...
2022-12-19 14:35:16,542 - INFO: Extending finished.

2022-12-19 14:35:16,918 - INFO: Separating extended fastq file ... 
2022-12-19 14:35:16,922 - INFO: Setting '-k 21,55,85,115'
2022-12-19 14:35:16,922 - INFO: Assembling using SPAdes ...
2022-12-19 14:35:16,931 - INFO: spades.py -t 1  --phred-offset 33 -1 ../../HN00176099_hdd1/mitogenomes/Tbolo_111_mitogenome/extended_1_paired.fq -2 ../../HN00176099_hdd1/mitogenomes/Tbolo_111_mitogenome/extended_2_paired.fq --s1 ../../HN00176099_hdd1/mitogenomes/Tbolo_111_mitogenome/extended_1_unpaired.fq --s2 ../../HN00176099_hdd1/mitogenomes/Tbolo_111_mitogenome/extended_2_unpaired.fq -k 21,55,85,115 -o ../../HN00176099_hdd1/mitogenomes/Tbolo_111_mitogenome/extended_spades
2022-12-19 14:35:28,495 - ERROR: Error with running SPAdes: == Error ==  system call for: "['/uufs/chpc.utah.edu/sys/installdir/r8/spades/3.15.4/bin/spades-core', '/uufs/chpc.utah.edu/common/home/gompert-group3/projects/troglo_SPY/HN00176099_hdd1/mitogenomes/Tbolo_111_mitogenome/extended_spades/K115/configs/config.info']" finished abnormally, OS return value: 21
2022-12-19 14:35:28,508 - ERROR: Assembling failed.

Total cost 353.11 s
Thank you!