a problem with plascope

[andrenalina1]

Hello

I am trying to use this program for the first time. I am using it with a genome.fasta obtained by unicycle (de novo assembly). Then the plascope run, the result is that nothing can be classified. By other programs, I determinate the sequence of a plasmid in this bacterial genome, which corresponds to the entire contig 24. I wanted to use this program to determine the presence of more plasmids and the chromosome contigs. Could you tell me what I'm doing wrong? These are the commands I used and the result

*commands

plaScope.sh --fasta EC_mcr1.fasta -o ~/sep2023/genome/ --db_dir /home/aaguilar/sep2023/genome/chromosome_plasmid_db/ --db_name chromosome_plasmid_db --sample predictions_8

*I obtained

Step 1: Contigs classification with Centrifuge and custom database
Centrifuge log can be found here: /home/aaguilar/sep2023/genome/predictions_8_PlaScope/Centrifuge_results/centrifuge.log
Step 2: Extraction of plasmid, chromosome and unclassified predictions
Warning: >1 length=505871 depth=0.94x not classified.
Warning: >2 length=440556 depth=0.99x not classified.
Warning: >3 length=321750 depth=1.00x not classified.
Warning: >4 length=311573 depth=1.02x not classified.
Warning: >5 length=289527 depth=1.04x not classified.
Warning: >6 length=228398 depth=1.02x not classified.
Warning: >7 length=224191 depth=1.04x not classified.
Warning: >8 length=192977 depth=0.95x not classified.
Warning: >9 length=184960 depth=1.08x not classified.
Warning: >10 length=178658 depth=0.97x not classified.
Warning: >11 length=168364 depth=0.97x not classified.
Warning: >12 length=152638 depth=1.04x not classified.
Warning: >13 length=141975 depth=1.05x not classified.
Warning: >14 length=139357 depth=1.06x not classified.
Warning: >15 length=133415 depth=0.98x not classified.
Warning: >16 length=114644 depth=0.95x not classified.
Warning: >17 length=92483 depth=0.99x not classified.
Warning: >18 length=86564 depth=1.03x not classified.
Warning: >19 length=78165 depth=1.01x not classified.
Warning: >20 length=72819 depth=1.03x not classified.
Warning: >21 length=70475 depth=1.03x not classified.
Warning: >22 length=67770 depth=0.95x not classified.
Warning: >23 length=66290 depth=1.06x not classified.
Warning: >24 length=60943 depth=0.89x circular=true not classified.
Warning: >25 length=58754 depth=1.06x not classified.
Warning: >26 length=55719 depth=1.00x not classified.
Warning: >27 length=54203 depth=1.06x not classified.
Warning: >28 length=42958 depth=1.43x not classified.
Warning: >29 length=41573 depth=1.05x not classified.
Warning: >30 length=41168 depth=1.00x not classified.
Warning: >31 length=39158 depth=0.96x not classified.
Warning: >32 length=38737 depth=1.59x not classified.
Warning: >33 length=30013 depth=1.08x not classified.
Warning: >34 length=27569 depth=0.95x not classified.
Warning: >35 length=26933 depth=0.98x not classified.
Warning: >36 length=22628 depth=1.03x not classified.
Warning: >37 length=19698 depth=1.49x not classified.
Warning: >38 length=19688 depth=0.94x not classified.
Warning: >39 length=19269 depth=1.16x not classified.
Warning: >40 length=18705 depth=1.09x not classified.
Warning: >41 length=16851 depth=1.09x not classified.
Warning: >42 length=16823 depth=1.07x not classified.
Warning: >43 length=16597 depth=1.63x not classified.
Warning: >44 length=15719 depth=1.45x not classified.
Warning: >45 length=12419 depth=1.00x not classified.
Warning: >46 length=11963 depth=1.56x not classified.
Warning: >47 length=10631 depth=1.52x not classified.
Warning: >48 length=9055 depth=1.02x not classified.
Warning: >49 length=9025 depth=1.59x not classified.
Warning: >50 length=8375 depth=1.48x not classified.
Warning: >51 length=8318 depth=1.44x not classified.
Warning: >52 length=7399 depth=1.60x not classified.
Warning: >53 length=6647 depth=8.03x circular=true not classified.
Warning: >54 length=6569 depth=1.45x not classified.
Warning: >55 length=5335 depth=1.49x not classified.
Warning: >56 length=5307 depth=1.14x not classified.
Warning: >57 length=5014 depth=1.54x not classified.
Warning: >58 length=4888 depth=1.08x not classified.
Warning: >59 length=4860 depth=1.03x not classified.
Warning: >60 length=4773 depth=7.42x circular=true not classified.
Warning: >61 length=4506 depth=1.01x not classified.
Warning: >62 length=4440 depth=1.04x not classified.
Warning: >63 length=4405 depth=0.89x not classified.
Warning: >64 length=4265 depth=2.19x not classified.
Warning: >65 length=3893 depth=1.57x not classified.
Warning: >66 length=3791 depth=1.52x not classified.
Warning: >67 length=3751 depth=21.71x circular=true not classified.
Warning: >68 length=3177 depth=51.43x circular=true not classified.
Warning: >69 length=2903 depth=1.66x not classified.
Warning: >70 length=2810 depth=3.49x not classified.
Warning: >71 length=2764 depth=1.06x not classified.
Warning: >72 length=2735 depth=1.42x not classified.
Warning: >73 length=2587 depth=1.46x not classified.
Warning: >74 length=2462 depth=6.21x not classified.
Warning: >75 length=2255 depth=1.51x not classified.
Warning: >76 length=2222 depth=7.34x not classified.
Warning: >77 length=1911 depth=1.50x not classified.
Warning: >78 length=1838 depth=1.81x not classified.
Warning: >79 length=1702 depth=7.44x not classified.
Warning: >80 length=1552 depth=87.93x circular=true not classified.
Warning: >81 length=1443 depth=2.00x not classified.
Warning: >82 length=1378 depth=3.11x not classified.
Warning: >83 length=1374 depth=2.12x not classified.
Warning: >84 length=1276 depth=1.98x not classified.
Warning: >85 length=1224 depth=0.94x not classified.
Warning: >86 length=1205 depth=0.93x not classified.
Warning: >87 length=1195 depth=1.99x not classified.
Warning: >88 length=1188 depth=6.94x not classified.
Warning: >89 length=1171 depth=2.47x not classified.
Warning: >90 length=1150 depth=1.53x not classified.
Warning: >91 length=1096 depth=1.33x not classified.
Warning: >92 length=1095 depth=1.80x not classified.
Warning: >93 length=1079 depth=1.96x not classified.
Warning: >94 length=1040 depth=1.54x not classified.
Warning: >95 length=1006 depth=16.37x not classified.
Warning: >96 length=986 depth=1.67x not classified.
Warning: >97 length=985 depth=1.20x not classified.
Warning: >98 length=985 depth=1.26x not classified.
Warning: >99 length=956 depth=2.04x not classified.
Warning: >100 length=848 depth=0.99x not classified.
Warning: >101 length=823 depth=4.17x not classified.
Warning: >102 length=822 depth=3.18x not classified.
Warning: >103 length=809 depth=1.79x not classified.
Warning: >104 length=797 depth=7.61x not classified.
Warning: >105 length=762 depth=1.65x not classified.
Warning: >106 length=748 depth=1.45x not classified.
Warning: >107 length=748 depth=1.48x not classified.
Warning: >108 length=737 depth=4.29x not classified.
Warning: >109 length=723 depth=1.75x not classified.
Warning: >110 length=723 depth=1.65x not classified.
Warning: >111 length=607 depth=3.18x not classified.
Warning: >112 length=606 depth=0.87x not classified.
Warning: >113 length=597 depth=3.18x not classified.
Warning: >114 length=553 depth=0.91x not classified.
Warning: >115 length=536 depth=1.51x not classified.
Warning: >116 length=458 depth=3.31x not classified.
Warning: >117 length=454 depth=4.36x not classified.
Warning: >118 length=422 depth=3.56x not classified.
Warning: >119 length=387 depth=4.44x not classified.
Warning: >120 length=377 depth=2.89x not classified.
Warning: >121 length=348 depth=0.98x not classified.
Warning: >122 length=343 depth=0.88x not classified.
Warning: >123 length=335 depth=0.88x not classified.
Warning: >124 length=328 depth=1.00x not classified.
Warning: >125 length=327 depth=1.08x not classified.
Warning: >126 length=320 depth=3.51x not classified.
Warning: >127 length=316 depth=1.65x not classified.
Warning: >128 length=265 depth=1.05x not classified.
Warning: >129 length=260 depth=1.14x not classified.
Warning: >130 length=259 depth=1.07x not classified.
Warning: >131 length=242 depth=13.01x not classified.
Warning: >132 length=224 depth=2.82x not classified.
Warning: >133 length=219 depth=0.86x not classified.
Warning: >134 length=203 depth=1.20x not classified.
Warning: >135 length=189 depth=3.62x not classified.
Warning: >136 length=184 depth=1.36x not classified.
Warning: >137 length=181 depth=1.82x not classified.
Warning: >138 length=175 depth=3.63x not classified.
Warning: >139 length=173 depth=3.03x not classified.
Warning: >140 length=170 depth=2.06x not classified.
Warning: >141 length=168 depth=0.54x not classified.
Warning: >142 length=164 depth=1.52x not classified.
Warning: >143 length=163 depth=2.74x not classified.
Warning: >144 length=152 depth=2.50x not classified.
Warning: >145 length=152 depth=3.71x not classified.
Warning: >146 length=149 depth=2.12x not classified.
Warning: >147 length=136 depth=2.10x not classified.
Warning: >148 length=135 depth=9.14x not classified.
Warning: >149 length=135 depth=4.65x not classified.
Warning: >150 length=134 depth=12.94x not classified.
Warning: >151 length=134 depth=1.74x not classified.
Warning: >152 length=132 depth=1.17x not classified.
Warning: >153 length=130 depth=4.65x not classified.
Warning: >154 length=128 depth=1.83x not classified.
Warning: >155 length=128 depth=1.58x not classified.
Warning: >156 length=108 depth=0.97x not classified.
Warning: >157 length=105 depth=6.29x not classified.
Warning: >158 length=103 depth=1.74x not classified.
Warning: >159 length=103 depth=6.95x not classified.
Warning: >160 length=103 depth=5.26x not classified.
Warning: >161 length=100 depth=1.33x not classified.

[GuilhemRoyer]

Hi andrenalina1,

Glad you're using Plascope. I think your command is missing the "-a" option to specify the assembler.

You should try the following command:

plaScope.sh --fasta EC_mcr1.fasta -o ~/sep2023/genome/ --db_dir /home/aaguilar/sep2023/genome/chromosome_plasmid_db/ --db_name chromosome_plasmid_db --sample predictions_8 -a unicycler

Please let me know if it works.

Best,

[andrenalina1]

hello
First, thanks for the response. I tried adding -a unicycler, but it didn't work. It only returned this

usage: plaScope.sh [OPTIONS] [ARGUMENTS]
General options:
-h, --help display this message and exit
-v, --version display version number and exit
-n, --no-banner don't print beautiful banners
-t number of threads[OPTIONAL] [default : 8]
-o output directory [OPTIONAL] [default : current directory]
--sample Sample name [MANDATORY]
--db_dir path to centrifuge database [MANDATORY]
--db_name centrifuge database name [MANDATORY]

Mode 1: SPAdes assembly + contig classification
-1 forward paired-end reads [MANDATORY]
-2 reverse paired-end reads [MANDATORY]
Mode 2: contig classification of a fasta file (only if you already have your SPAdes assembly!)
--fasta SPAdes assembly fasta file [MANDATORY]

Example mode 1:
plaScope.sh -1 my_reads_1.fastq.gz -2 my_reads_2.fastq.gz -o output_directory --db_dir path/to/DB --db_name chromosome_plasmid_db --sample name_of_my_sample
Example mode 2:
plaScope.sh --fasta my_fastafile.fasta -o output_directory --db_dir path/to/DB --db_name chromosome_plasmid_db --sample name_of_my_sample
Github:
https://github.com/GuilhemRoyer/PlaScope

I installed the program from bioconda, I just saw that version 1.3 was installed. Does it have anything to do with this problem?

[GuilhemRoyer]

Ok, maybe there's a problem with the current version of PlaScope... We need to look into this further.

Anyway, I'm pretty sure the problem is with your contig names. PlaScope uses the coverage and length of the contig header to filter the results. To test this hypothesis, you can try changing the names of your contigs using the following (dirty) command, then launch PlaScope.

sed 's/>/>NODE_/g' [your_file.fasta] | sed 's/ length=/length/g' | sed 's/ depth=/cov/g' | sed 's/x//g' | sed 's/.//g' > [your_file_modified.fasta]

[andrenalina1]

thank you. I tried to use it but the output file is empty, I am trying to modify the command to make it work. On the other hand, I tell you that the file has the following format for the contigs

1 length=505871 depth=0.94x

and for those who unicycler closed in circular contigs

24 length=60943 depth=0.89x circular=true

[GuilhemRoyer]

Ok. Can you attach part of your fasta file (e.g, 2 or 3 contigs) so I can try modify it and send it back to you?

[andrenalina1]

Yes, I attached the file. Thank you very much for the help

sequence_ecoli.txt

[GuilhemRoyer]

Sorry there was a mistake in my command line. Please try the following one on your fasta file :

sed 's/>/>NODE_/g' [your_file.fasta] | sed 's/ length=/length/g' | sed 's/ depth=/cov/g' | sed 's/x//g' | sed 's/.//g' | sed 's/ circular.*//g' > [your_file_modified.fasta]

Then run the mode 2 of PlaScope with the option -a spades

[alex-trist]

Hi!

I'm experiencing a similar issue to the one presented by @andrenalina1. All contings returned as unclassified. I'm using plaScope on mode 2, with assembled reads from unicyler v0.5.0. I installed plascope using conda, but replaced the main script (plaScope.sh) since it seemed to be outdated (no -a option on the script). I already tried reformating my contigs using @GuilhemRoyer commad, but the problem persists. Any other ideas on how ti fix it?
Thanks in advance,

*commands

plaScope.sh --fasta contigs/EC1006465.fasta -o plascope/ --db_dir ../Data_Bases/plascope_db/ --db_name chromosome_plasmid_db --sample EC1006465 -a unicycler

*results

Warning: >1 length=636770 depth=0.95x not classified.
Warning: >2 length=367827 depth=1.11x not classified.
Warning: >3 length=356735 depth=0.95x not classified.
Warning: >4 length=318082 depth=1.09x not classified.
Warning: >5 length=292964 depth=0.90x not classified.
Warning: >6 length=269713 depth=1.03x not classified.
Warning: >7 length=246032 depth=0.89x not classified.
Warning: >8 length=239686 depth=1.00x not classified.
Warning: >9 length=201086 depth=1.06x not classified.
Warning: >10 length=190833 depth=1.12x not classified.
Warning: >11 length=150742 depth=1.14x not classified.
Warning: >12 length=144284 depth=0.85x not classified.
Warning: >13 length=137432 depth=1.14x not classified.
Warning: >14 length=134346 depth=1.01x not classified.
Warning: >15 length=133038 depth=1.13x not classified.
Warning: >16 length=127739 depth=1.05x not classified.
Warning: >17 length=109005 depth=1.15x not classified.
Warning: >18 length=105708 depth=1.06x not classified.
Warning: >19 length=56157 depth=1.03x not classified.
Warning: >20 length=52304 depth=0.93x not classified.
Warning: >21 length=50856 depth=1.22x not classified.
Warning: >22 length=46658 depth=0.86x not classified.
Warning: >23 length=42494 depth=0.85x not classified.
Warning: >24 length=41261 depth=1.12x not classified.
Warning: >25 length=38536 depth=1.10x not classified.
Warning: >26 length=36134 depth=1.06x not classified.
Warning: >27 length=35026 depth=0.98x not classified.
Warning: >28 length=33549 depth=0.93x not classified.
Warning: >29 length=32592 depth=1.12x not classified.
Warning: >30 length=31679 depth=1.05x not classified.
Warning: >31 length=29665 depth=1.14x not classified.
Warning: >32 length=28205 depth=0.82x not classified.
Warning: >33 length=25327 depth=0.92x not classified.
Warning: >34 length=23590 depth=1.06x not classified.
Warning: >35 length=20026 depth=1.09x not classified.
Warning: >36 length=16232 depth=1.03x not classified.
Warning: >37 length=15724 depth=0.90x not classified.
Warning: >38 length=13205 depth=0.93x not classified.
Warning: >39 length=11201 depth=1.18x not classified.
Warning: >40 length=11155 depth=1.26x not classified.
Warning: >41 length=11004 depth=1.15x not classified.
Warning: >42 length=10586 depth=1.04x not classified.
Warning: >43 length=10524 depth=1.26x not classified.
Warning: >44 length=8758 depth=1.12x not classified.
Warning: >45 length=7103 depth=1.23x not classified.
Warning: >46 length=6717 depth=0.89x not classified.
Warning: >47 length=4115 depth=1.16x not classified.
Warning: >48 length=4063 depth=4.90x circular=true not classified.
Warning: >49 length=3716 depth=1.19x not classified.
Warning: >50 length=3699 depth=0.94x not classified.
Warning: >51 length=3581 depth=1.21x not classified.
Warning: >52 length=3232 depth=1.24x not classified.
Warning: >53 length=3086 depth=8.11x not classified.
Warning: >54 length=3034 depth=1.33x not classified.
Warning: >55 length=2733 depth=1.13x not classified.
Warning: >56 length=2581 depth=3.11x not classified.
Warning: >57 length=2532 depth=2.99x not classified.
Warning: >58 length=2242 depth=0.91x not classified.
Warning: >59 length=2231 depth=1.15x not classified.
Warning: >60 length=1740 depth=1.30x not classified.
Warning: >61 length=1425 depth=8.31x not classified.
Warning: >62 length=1344 depth=1.23x not classified.
Warning: >63 length=1259 depth=0.99x not classified.
Warning: >64 length=1103 depth=1.08x not classified.
Warning: >65 length=1045 depth=0.97x not classified.
Warning: >66 length=1017 depth=2.09x not classified.
Warning: >67 length=985 depth=3.74x not classified.
Warning: >68 length=963 depth=2.23x not classified.
Warning: >69 length=892 depth=1.04x not classified.
Warning: >70 length=881 depth=2.45x not classified.
Warning: >71 length=879 depth=0.91x not classified.
Warning: >72 length=861 depth=0.80x not classified.
Warning: >73 length=861 depth=0.84x not classified.
Warning: >74 length=859 depth=2.10x not classified.
Warning: >75 length=834 depth=0.97x not classified.
Warning: >76 length=834 depth=0.99x not classified.
Warning: >77 length=796 depth=1.12x not classified.
Warning: >78 length=757 depth=1.13x not classified.
Warning: >79 length=754 depth=1.99x not classified.
Warning: >80 length=740 depth=2.21x not classified.
Warning: >81 length=712 depth=0.95x not classified.
Warning: >82 length=691 depth=1.86x not classified.
Warning: >83 length=671 depth=2.39x not classified.
Warning: >84 length=647 depth=1.90x not classified.
Warning: >85 length=620 depth=1.01x not classified.
Warning: >86 length=592 depth=1.21x not classified.
Warning: >87 length=518 depth=2.21x not classified.
Warning: >88 length=480 depth=1.03x not classified.
Warning: >89 length=480 depth=0.73x not classified.
Warning: >90 length=477 depth=0.79x not classified.
Warning: >91 length=438 depth=2.48x not classified.
Warning: >92 length=436 depth=1.17x not classified.
Warning: >93 length=436 depth=0.99x not classified.
Warning: >94 length=431 depth=1.04x not classified.
Warning: >95 length=402 depth=1.71x not classified.
Warning: >96 length=389 depth=2.06x not classified.
Warning: >97 length=378 depth=0.92x not classified.
Warning: >98 length=378 depth=0.87x not classified.
Warning: >99 length=356 depth=3.44x not classified.
Warning: >100 length=346 depth=17.27x not classified.
Warning: >101 length=340 depth=3.39x not classified.
Warning: >102 length=337 depth=1.15x not classified.
Warning: >103 length=336 depth=0.96x not classified.
Warning: >104 length=336 depth=1.01x not classified.
Warning: >105 length=334 depth=0.91x not classified.
Warning: >106 length=334 depth=1.02x not classified.
Warning: >107 length=332 depth=2.10x not classified.
Warning: >108 length=329 depth=1.28x not classified.
Warning: >109 length=313 depth=1.03x not classified.
Warning: >110 length=313 depth=0.91x not classified.
Warning: >111 length=294 depth=1.15x not classified.
Warning: >112 length=287 depth=1.20x not classified.
Warning: >113 length=281 depth=1.01x not classified.
Warning: >114 length=274 depth=0.75x not classified.
Warning: >115 length=272 depth=0.96x not classified.
Warning: >116 length=272 depth=0.89x not classified.
Warning: >117 length=270 depth=2.49x not classified.
Warning: >118 length=265 depth=4.11x not classified.
Warning: >119 length=262 depth=1.04x not classified.
Warning: >120 length=262 depth=0.70x not classified.
Warning: >121 length=256 depth=0.86x not classified.
Warning: >122 length=247 depth=2.06x not classified.
Warning: >123 length=241 depth=1.58x not classified.
Warning: >124 length=241 depth=2.38x not classified.
Warning: >125 length=237 depth=0.99x not classified.
Warning: >126 length=237 depth=2.74x not classified.
Warning: >127 length=228 depth=1.02x not classified.
Warning: >128 length=221 depth=1.16x not classified.
Warning: >129 length=219 depth=1.69x not classified.
Warning: >130 length=216 depth=1.62x not classified.
Warning: >131 length=214 depth=2.17x not classified.
Warning: >132 length=214 depth=0.77x not classified.
Warning: >133 length=212 depth=2.01x not classified.
Warning: >134 length=211 depth=0.83x not classified.
Warning: >135 length=211 depth=1.04x not classified.
Warning: >136 length=202 depth=0.92x not classified.
Warning: >137 length=197 depth=1.36x not classified.
Warning: >138 length=197 depth=1.10x not classified.
Warning: >139 length=193 depth=1.99x not classified.
Warning: >140 length=192 depth=2.50x not classified.
Warning: >141 length=192 depth=1.35x not classified.
Warning: >142 length=190 depth=2.25x not classified.
Warning: >143 length=187 depth=2.05x not classified.
Warning: >144 length=181 depth=1.99x not classified.
Warning: >145 length=176 depth=1.63x not classified.
Warning: >146 length=173 depth=1.17x not classified.
Warning: >147 length=173 depth=1.58x not classified.
Warning: >148 length=173 depth=0.94x not classified.
Warning: >149 length=173 depth=1.52x not classified.
Warning: >150 length=171 depth=1.15x not classified.
Warning: >151 length=171 depth=0.74x not classified.
Warning: >152 length=171 depth=3.41x not classified.
Warning: >153 length=164 depth=3.68x not classified.
Warning: >154 length=161 depth=2.23x not classified.
Warning: >155 length=160 depth=0.72x not classified.
Warning: >156 length=160 depth=0.72x not classified.
Warning: >157 length=160 depth=1.11x not classified.
Warning: >158 length=158 depth=2.07x not classified.
Warning: >159 length=157 depth=0.85x not classified.
Warning: >160 length=157 depth=1.25x not classified.
Warning: >161 length=156 depth=1.10x not classified.
Warning: >162 length=156 depth=0.88x not classified.
Warning: >163 length=154 depth=2.84x not classified.
Warning: >164 length=152 depth=2.15x not classified.
Warning: >165 length=152 depth=2.93x not classified.
Warning: >166 length=151 depth=2.55x not classified.
Warning: >167 length=151 depth=7.81x not classified.
Warning: >168 length=150 depth=2.07x not classified.
Warning: >169 length=149 depth=2.26x not classified.
Warning: >170 length=149 depth=5.20x not classified.
Warning: >171 length=146 depth=1.66x not classified.
Warning: >172 length=145 depth=1.74x not classified.
Warning: >173 length=142 depth=0.91x not classified.
Warning: >174 length=141 depth=1.62x not classified.
Warning: >175 length=140 depth=2.08x not classified.
Warning: >176 length=140 depth=0.92x not classified.
Warning: >177 length=139 depth=0.83x not classified.
Warning: >178 length=138 depth=3.26x not classified.
Warning: >179 length=136 depth=0.94x not classified.
Warning: >180 length=136 depth=1.14x not classified.
Warning: >181 length=135 depth=0.92x not classified.
Warning: >182 length=134 depth=0.93x not classified.
Warning: >183 length=134 depth=1.68x not classified.
Warning: >184 length=132 depth=3.04x not classified.
Warning: >185 length=131 depth=1.36x not classified.
Warning: >186 length=130 depth=1.13x not classified.
Warning: >187 length=130 depth=1.00x not classified.
Warning: >188 length=129 depth=1.78x not classified.
Warning: >189 length=129 depth=0.97x not classified.
Warning: >190 length=128 depth=1.77x not classified.
Warning: >191 length=128 depth=1.54x not classified.
Warning: >192 length=127 depth=0.86x not classified.
Warning: >193 length=127 depth=1.29x not classified.
Warning: >194 length=127 depth=1.00x not classified.
Warning: >195 length=127 depth=2.58x not classified.
Warning: >196 length=126 depth=1.50x not classified.
Warning: >197 length=126 depth=1.31x not classified.
Warning: >198 length=125 depth=2.29x not classified.
Warning: >199 length=125 depth=1.36x not classified.
Warning: >200 length=123 depth=3.12x not classified.
Warning: >201 length=122 depth=2.53x not classified.
Warning: >202 length=121 depth=2.13x not classified.
Warning: >203 length=120 depth=1.15x not classified.
Warning: >204 length=119 depth=1.39x not classified.
Warning: >205 length=118 depth=1.01x not classified.
Warning: >206 length=118 depth=1.24x not classified.
Warning: >207 length=118 depth=2.17x not classified.
Warning: >208 length=116 depth=1.31x not classified.
Warning: >209 length=114 depth=2.15x not classified.
Warning: >210 length=113 depth=1.63x not classified.
Warning: >211 length=113 depth=3.17x not classified.
Warning: >212 length=113 depth=0.76x not classified.
Warning: >213 length=113 depth=2.66x not classified.
Warning: >214 length=113 depth=1.90x not classified.
Warning: >215 length=113 depth=0.95x not classified.
Warning: >216 length=112 depth=2.90x not classified.
Warning: >217 length=111 depth=2.12x not classified.
Warning: >218 length=110 depth=1.12x not classified.
Warning: >219 length=110 depth=1.88x not classified.
Warning: >220 length=108 depth=1.10x not classified.
Warning: >221 length=108 depth=0.81x not classified.
Warning: >222 length=108 depth=2.36x not classified.
Warning: >223 length=105 depth=2.25x not classified.
Warning: >224 length=105 depth=1.94x not classified.
Warning: >225 length=105 depth=1.43x not classified.
Warning: >226 length=104 depth=1.34x not classified.
Warning: >227 length=104 depth=2.31x not classified.
Warning: >228 length=104 depth=1.75x not classified.
Warning: >229 length=103 depth=5.93x not classified.
Warning: >230 length=102 depth=0.96x not classified.
Warning: >231 length=102 depth=3.47x not classified.
Warning: >232 length=102 depth=1.33x not classified.
Warning: >233 length=102 depth=2.52x not classified.
Warning: >234 length=101 depth=2.76x not classified.
Warning: >235 length=101 depth=2.53x not classified.
Warning: >236 length=101 depth=11.93x not classified.
Warning: >237 length=101 depth=1.65x not classified.

centrifuge.log