Slimming fails

[Tmesipteris]

Can I please have some help with an error I am getting. I installed GetOrganelle on ubuntu. For some reason the runs do not complete with an error appearing that says that slimming has failed. I have pasted the log below. Any help with resolving this issue would be much appreciated.

Python 3.7.0 (default, Jun 28 2018, 13:15:42) [GCC 7.2.0]
PYTHON LIBS: GetOrganelleLib 1.7.1a; numpy 1.19.1; sympy 1.6.2; scipy 1.5.2
DEPENDENCIES: Bowtie2 2.3.4.1; SPAdes 3.11.1; Blast 2.6.0
LABEL DB: embplant_pt 0.0.0; embplant_mt 0.0.0
WORKING DIR: /mnt/j/BGI shotgun sequence data August 13th 2020/Kurobe-17 Higashiakaishi
/home/james/miniconda3/bin/get_organelle_from_reads.py -1 V300068204_L2_THUtakRBAAB-608_1.fq -2 V300068204_L2_THUtakRBAAB-608_2.fq -s KX832627.fasta -o Kurobe17_output -R 15 -k 21,45,65,85,105 -F embplant_pt

2020-08-19 08:38:24,198 - INFO: Pre-reading fastq ...
2020-08-19 08:38:24,200 - INFO: Estimating reads to use ... (to use all reads, set '--reduce-reads-for-coverage inf')
2020-08-19 08:38:24,764 - INFO: Tasting 100000+100000 reads ...
2020-08-19 08:38:35,643 - INFO: Estimating reads to use finished.
2020-08-19 08:39:31,329 - INFO: Counting read qualities ...
2020-08-19 08:39:31,521 - INFO: Identified quality encoding format = Sanger
2020-08-19 08:39:31,523 - INFO: Trimming bases with qualities (0.00%): 33..33 !
2020-08-19 08:39:31,601 - INFO: Mean error rate = 0.0029
2020-08-19 08:39:31,603 - INFO: Counting read lengths ...
2020-08-19 08:39:47,957 - INFO: Mean = 150.0 bp, maximum = 150 bp.
2020-08-19 08:39:47,958 - INFO: Reads used = 4114149+4114149
2020-08-19 08:39:47,958 - INFO: Pre-reading fastq finished.

2020-08-19 08:39:47,959 - INFO: Making seed reads ...
2020-08-19 08:39:48,137 - INFO: Seed bowtie2 index existed!
2020-08-19 08:39:48,140 - INFO: Mapping reads to seed bowtie2 index ...
2020-08-19 08:41:11,502 - INFO: Mapping finished.
2020-08-19 08:41:11,503 - INFO: Seed reads made: Kurobe17_output/seed/embplant_pt.initial.fq (31862520 bytes)
2020-08-19 08:41:11,504 - INFO: Making seed reads finished.

2020-08-19 08:41:11,505 - INFO: Checking seed reads and parameters ...
2020-08-19 08:41:11,505 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2020-08-19 08:41:11,506 - INFO: If the result graph is not a circular organelle genome,
2020-08-19 08:41:11,506 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2020-08-19 08:41:16,591 - INFO: Pre-assembling mapped reads ...
2020-08-19 08:43:08,014 - WARNING: Pre-assembling failed. The estimations for embplant_pt-hitting base-coverage and word size may be misleading.
2020-08-19 08:43:08,210 - INFO: Estimated embplant_pt-hitting base-coverage = 140.21
2020-08-19 08:43:08,680 - INFO: Estimated word size(s): 93
2020-08-19 08:43:08,681 - INFO: Setting '-w 93'
2020-08-19 08:43:08,681 - INFO: Setting '--max-extending-len inf'
2020-08-19 08:43:08,875 - INFO: Checking seed reads and parameters finished.

2020-08-19 08:43:08,876 - INFO: Making read index ...
2020-08-19 08:44:36,113 - INFO: 8150988 candidates in all 8228298 reads
2020-08-19 08:44:36,133 - INFO: Pre-grouping reads ...
2020-08-19 08:44:36,133 - INFO: Setting '--pre-w 93'
2020-08-19 08:44:36,814 - INFO: 39166/39166 used/duplicated
2020-08-19 08:44:50,366 - INFO: 636 groups made.
2020-08-19 08:44:51,754 - INFO: Making read index finished.

2020-08-19 08:44:51,755 - INFO: Extending ...
2020-08-19 08:44:51,755 - INFO: Adding initial words ...
2020-08-19 08:44:55,606 - INFO: AW 1768366
2020-08-19 08:45:55,492 - INFO: Round 1: 8150988/8150988 AI 78952 AW 1794490
2020-08-19 08:46:53,491 - INFO: Round 2: 8150988/8150988 AI 78993 AW 1795090
2020-08-19 08:47:52,515 - INFO: Round 3: 8150988/8150988 AI 78993 AW 1795090
2020-08-19 08:47:52,515 - INFO: No more reads found and terminated ...
2020-08-19 08:48:12,527 - INFO: Extending finished.

2020-08-19 08:48:12,761 - INFO: Separating filtered fastq file ...
2020-08-19 08:48:13,918 - INFO: Setting '-k 21,45,65,85,105'
2020-08-19 08:48:13,919 - INFO: Assembling using SPAdes ...
2020-08-19 08:48:13,975 - INFO: spades.py -t 1 -1 Kurobe17_output/filtered_1_paired.fq -2 Kurobe17_output/filtered_2_paired.fq --s1 Kurobe17_output/filtered_1_unpaired.fq --s2 Kurobe17_output/filtered_2_unpaired.fq -k 21,45,65,85,105 -o Kurobe17_output/filtered_spades
2020-08-19 08:49:33,763 - INFO: Insert size = 336.832, deviation = 76.2638, left quantile = 237, right quantile = 432
2020-08-19 08:49:33,764 - INFO: Assembling finished.

2020-08-19 08:49:35,344 - ERROR: Slimming Kurobe17_output/filtered_spades/K105/assembly_graph.fastg failed. Please check Kurobe17_output/filtered_spades/K105/slim.log.txt for details.
2020-08-19 08:49:36,660 - ERROR: Slimming Kurobe17_output/filtered_spades/K85/assembly_graph.fastg failed. Please check Kurobe17_output/filtered_spades/K85/slim.log.txt for details.
2020-08-19 08:49:38,037 - ERROR: Slimming Kurobe17_output/filtered_spades/K65/assembly_graph.fastg failed. Please check Kurobe17_output/filtered_spades/K65/slim.log.txt for details.
2020-08-19 08:49:39,339 - ERROR: Slimming Kurobe17_output/filtered_spades/K45/assembly_graph.fastg failed. Please check Kurobe17_output/filtered_spades/K45/slim.log.txt for details.
2020-08-19 08:49:39,341 - ERROR: No valid assembly graph found!

Total cost 677.74 s
Thank you!

[Tmesipteris]

Problem solved. It was because there were spaces in the directory. Replaced these with _ and it worked.