TypeError: a bytes-like object is required, not 'str'

[Bei Gao]

Hi,

I just installed kneaddata and ran the demo data successfully. However when I run the following command on my own data, a error message occurred. Thanks a lot for the help!

kneaddata --input Data/RawFastQ/10-003-P1_S1_R1_001.fastq --input Data/RawFastQ/10-003-P1_S1_R2_001.fastq -db HumanGenomeDatabase/Homo_sapiens --output kneaddata_output_10

Below is the standard error:

Traceback (most recent call last):

  File "/home/wintergb/.local/bin/kneaddata", line 11, in <module>

    sys.exit(main())

  File "/home/wintergb/.local/lib/python3.5/site-packages/kneaddata/knead_data.py", line 427, in main

    args.input[index]=utilities.get_reformatted_identifiers(args.input[index],args.output_dir, temp_output_files)

  File "/home/wintergb/.local/lib/python3.5/site-packages/kneaddata/utilities.py", line 258, in get_reformatted_identifiers

    os.write(file_out, "".join(lines))

TypeError: a bytes-like object is required, not 'str'

Below is the log file:

10/04/2018 10:37:59 AM - kneaddata.knead_data - INFO: Running kneaddata v0.6.1

10/04/2018 10:37:59 AM - kneaddata.knead_data - INFO: Output files will be written to: /share/fiehnlab/users/bgao/kneaddata_output_10

10/04/2018 10:37:59 AM - kneaddata.knead_data - DEBUG: Running with the following arguments:

trimmomatic_quality_scores = -phred33

log_level = DEBUG

fastqc_path = None

serial = False

trimmomatic_path = /software/trimmomatic/0.33/static/trimmomatic-0.33.jar

pm = 80

bowtie2_path = /software/bowtie2/2.3.4.1/lssc0-linux/bowtie2

trimmomatic_options = None

reference_db = /share/fiehnlab/users/bgao/HumanGenomeDatabase/Homo_sapiens

threads = 1

pi = 10

bowtie2_options = --very-sensitive --phred33

bmtagger = False

output_prefix = 10-003-P1_S1_R1_001_kneaddata

no_discordant = False

log = /share/fiehnlab/users/bgao/kneaddata_output_10/10-003-P1_S1_R1_001_kneaddata.log

trf_path = None

trf = False

minscore = 50

bypass_trim = False

remove_temp_output = True

delta = 7

output_dir = /share/fiehnlab/users/bgao/kneaddata_output_10

verbose = False

maxperiod = 500

cat_final_output = False

cat_pairs = False

input = /share/fiehnlab/users/bgao/Data/RawFastQ/10-003-P1_S1_R1_001.fastq /share/fiehnlab/users/bgao/Data/RawFastQ/10-003-P1_S1_R2_001.fastq

fastqc_end = False

mismatch = 7

reorder = False

match = 2

remove_intermediate_output = False

processes = 1

max_memory = 500m

store_temp_output = False

bmtagger_path = None

fastqc_start = False

10/04/2018 10:37:59 AM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ...

[Drishti Kaul]

I think it has to do with the version of python you're using, it messes up with v3.5 and above. What version are you using?

[Bei Gao]

Thanks, Drishti! 

When I typed in python -V in my home directory, it showed Python 2.7.12.

However, the server I am using has different versions installed, including python 2, python 2.7, python 3.5 and python 3.5m. I didn't specify any version when I ran the above commands. 

[Bei Gao]

Oh, when I typed in python3 -V in my home directory, it showed Python 3.5.2. I am confused which one I was using...LOL