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Error_UnicodeDecodeError
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Error_UnicodeDecodeError
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Building a LARGE index
Renaming ../instrain_result/Porphyromonas_endodontalis/bt2/reference_database.fasta.bt2.3.bt2l.tmp to ../instrain_result/Porphyromonas_endodontalis/bt2/reference_database.fasta.bt2.3.bt2l
Renaming ../instrain_result/Porphyromonas_endodontalis/bt2/reference_database.fasta.bt2.4.bt2l.tmp to ../instrain_result/Porphyromonas_endodontalis/bt2/reference_database.fasta.bt2.4.bt2l
Renaming ../instrain_result/Porphyromonas_endodontalis/bt2/reference_database.fasta.bt2.1.bt2l.tmp to ../instrain_result/Porphyromonas_endodontalis/bt2/reference_database.fasta.bt2.1.bt2l
Renaming ../instrain_result/Porphyromonas_endodontalis/bt2/reference_database.fasta.bt2.2.bt2l.tmp to ../instrain_result/Porphyromonas_endodontalis/bt2/reference_database.fasta.bt2.2.bt2l
Renaming ../instrain_result/Porphyromonas_endodontalis/bt2/reference_database.fasta.bt2.rev.1.bt2l.tmp to ../instrain_result/Porphyromonas_endodontalis/bt2/reference_database.fasta.bt2.rev.1.bt2l
Renaming ../instrain_result/Porphyromonas_endodontalis/bt2/reference_database.fasta.bt2.rev.2.bt2l.tmp to ../instrain_result/Porphyromonas_endodontalis/bt2/reference_database.fasta.bt2.rev.2.bt2l
223861232 reads; of these:
223861232 (100.00%) were paired; of these:
223845193 (99.99%) aligned concordantly 0 times
2 (0.00%) aligned concordantly exactly 1 time
16037 (0.01%) aligned concordantly >1 times
----
223845193 pairs aligned concordantly 0 times; of these:
1 (0.00%) aligned discordantly 1 time
----
223845192 pairs aligned 0 times concordantly or discordantly; of these:
447690384 mates make up the pairs; of these:
447684889 (100.00%) aligned 0 times
7 (0.00%) aligned exactly 1 time
5488 (0.00%) aligned >1 times
0.01% overall alignment rate
You gave me a sam- I'm going to make it a .bam now
Converting ../instrain_result/Porphyromonas_endodontalis/bowtie2_result/s11_11.sam to ../instrain_result/Porphyromonas_endodontalis/bowtie2_result/s11_11.bam
sorting ../instrain_result/Porphyromonas_endodontalis/bowtie2_result/s11_11.bam
[bam_sort_core] merging from 9 files and 20 in-memory blocks...
Indexing ../instrain_result/Porphyromonas_endodontalis/bowtie2_result/s11_11.sorted.bam
***************************************************
..:: inStrain profile Step 1. Filter reads ::..
***************************************************
^MFiltering reads: 0%| | 0/39 [00:00<?, ?it/s]^MFiltering reads: 3%|▎ | 1/39 [00:29<18:22, 29.03s/it]^MFiltering reads: 100%|██████████| 39/39 [00:29<00:00, 1.88it/s]^MFiltering reads: 100%|██████████| 39/39 [00:29<00:00, 1.33it/s]
Scaffold to bin was made using .stb file
0 of 2 genomes have less than 1x estimated coverage
0 of the original 39 scaffolds are removed (0 have a low coverage genome; 0 have no genome)
8.3% of pairs and 100.0% of singletons were removed during filtering
15,488 read pairs remain (0.004646 Gbp)
***************************************************
.:: inStrain profile Step 2. Profile scaffolds ::..
***************************************************
Traceback (most recent call last):
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/bin/inStrain", line 31, in <module>
inStrain.controller.Controller().main(args)
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/inStrain/controller.py", line 54, in main
self.profile_operation(args)
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/inStrain/controller.py", line 86, in profile_operation
ProfileController(args).main()
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/inStrain/controller.py", line 155, in main
self.run_profile()
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/inStrain/controller.py", line 333, in run_profile
self.ISP = inStrain.profile.profile_bam(self.bam, self.fasta_db,
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/inStrain/profile/__init__.py", line 17, in profile_bam
return inStrain.profile.profile_controller.BamProfileController(
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/inStrain/profile/profile_controller.py", line 48, in main
self.gen_prof_args()
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/inStrain/profile/profile_controller.py", line 78, in gen_prof_args
self.gen_genes_args()
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/inStrain/profile/profile_controller.py", line 89, in gen_genes_args
scaff2geneinfo, scaff2gene2sequence = inStrain.GeneProfile.parse_genes(gene_file, **self.kwargs)
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/inStrain/GeneProfile.py", line 761, in parse_genes
return parse_prodigal_genes(gene_file_loc)
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/inStrain/GeneProfile.py", line 778, in parse_prodigal_genes
for record in SeqIO.parse(gene_fasta, 'fasta'):
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/Bio/SeqIO/__init__.py", line 661, in parse
for r in i:
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/Bio/SeqIO/FastaIO.py", line 176, in FastaIterator
for title, sequence in SimpleFastaParser(handle):
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/site-packages/Bio/SeqIO/FastaIO.py", line 45, in SimpleFastaParser
for line in handle:
File "/lustre1/g/aos_shihuang/tools/anaconda3/envs/inStrain/lib/python3.8/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xbb in position 3: invalid start byte