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LuyiTian / FLAMES

Full-length transcriptome splicing and mutation analysis
GNU General Public License v3.0
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Error during re-alignment #43

Closed sparthib closed 9 months ago

sparthib commented 9 months ago

Hello, FLAMES aligns my reads to the reference genome but during realignment I get this error:

### skip aligning reads to genome 2023-12-07 15:57:35
### read gene annotation 2023-12-07 15:57:35
remove similar transcripts in gene annotation: Counter({'duplicated_transcripts': 765})
### find isoforms 2023-12-07 15:59:27
Traceback (most recent call last):
  File "/users/sparthib/flames/python/bulk_long_pipeline.py", line 270, in <module>
    bulk_long_pipeline(args)
  File "/users/sparthib/flames/python/bulk_long_pipeline.py", line 202, in bulk_long_pipeline
    group_bam2isoform(genome_bam, isoform_gff3, tss_tes_stat, "", chr_to_blocks, gene_dict, transcript_to_junctions, transcript_dict, args.genomefa,
  File "/users/sparthib/flames/python/sc_longread.py", line 1115, in group_bam2isoform
    for c in get_fa(fa_f):
  File "/users/sparthib/flames/python/sc_longread.py", line 45, in get_fa
    for line in open(fn):
  File "/users/sparthib/.conda/envs/FLAMES/lib/python3.10/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

I cloned the flames package from github and this is my environment info:


#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.23.0               hd590300_0    conda-forge
ca-certificates           2023.11.17           hbcca054_0    conda-forge
editdistance              0.6.2           py310hc6cd4ac_2    conda-forge
htslib                    1.18                 h81da01d_0    bioconda
k8                        0.2.5                hdcf5f25_4    bioconda
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libblas                   3.9.0           20_linux64_openblas    conda-forge
libcblas                  3.9.0           20_linux64_openblas    conda-forge
libcurl                   8.4.0                hca28451_0    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_3    conda-forge
libgfortran-ng            13.2.0               h69a702a_3    conda-forge
libgfortran5              13.2.0               ha4646dd_3    conda-forge
libgomp                   13.2.0               h807b86a_3    conda-forge
liblapack                 3.9.0           20_linux64_openblas    conda-forge
libnghttp2                1.58.0               h47da74e_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.25          pthreads_h413a1c8_0    conda-forge
libsqlite                 3.44.2               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_3    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
minimap2                  2.26                 he4a0461_2    bioconda
ncurses                   6.4                  h59595ed_2    conda-forge
numpy                     1.26.2          py310hb13e2d6_0    conda-forge
openssl                   3.2.0                hd590300_1    conda-forge
pip                       23.3.1             pyhd8ed1ab_0    conda-forge
pysam                     0.22.0          py310h41dec4a_0    bioconda
python                    3.10.13         hd12c33a_0_cpython    conda-forge
python_abi                3.10                    4_cp310    conda-forge
readline                  8.2                  h8228510_1    conda-forge
samtools                  1.18                 h50ea8bc_1    bioconda
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Any pointers would be appreciated, thank you!

sparthib commented 9 months ago

this error arose due to my reference fasta file being gzipped. flames ran after unzipping the file for alignment.