Hi I am unable to run humann function on my fastq file. I am not able to figure out the error I get.
I am able to run most of my fastq file but for few of them I am getting 2 types of error message. For few of them I get below meesage when I run below code:
Error 1:
(biobakery) [kots2z@bmi-460g10-05 fastq3]$ humann --input MP00064_Latha_merged.fastq.gz --output MP00064_Latha_merged_output
Creating output directory: /scratch/kots2z/staph_files_neg/fastq3/MP00064_Latha_merged_output
Output files will be written to: /scratch/kots2z/staph_files_neg/fastq3/MP00064_Latha_merged_output
Decompressing gzipped file …
Critical Error: Unable to unzip input file: /scratch/kots2z/staph_files_neg/fastq3/MP00064_Latha_merged.fastq.gz
CRITICAL ERROR: Unable to use gzipped input file. Please check the format of the input file.
I tried doing less input_file.fastq.gz and able to view it and nothing seems out of order.
Below is the log file that was created:
0/12/2022 10:21:29 AM - humann.humann - INFO: Running humann v3.0.0.alpha.4
10/12/2022 10:21:29 AM - humann.humann - INFO: Output files will be written to: /scratch/kots2z/staph_files_neg/fastq3/MP00064_Latha_merged_output
10/12/2022 10:21:29 AM - humann.humann - INFO: Writing temp files to directory: /scratch/kots2z/staph_files_neg/fastq3/MP00064_Latha_merged_output/MP00064_Latha_merged_humann_temp
10/12/2022 10:21:29 AM - humann.utilities - INFO: File ( /scratch/kots2z/staph_files_neg/fastq3/MP00064_Latha_merged.fastq.gz ) is of format: fastq.gz
10/12/2022 10:21:29 AM - humann.utilities - INFO: Decompressing gzipped file …
For other few samples, I get below message:
Error 2:
(biobakery) [kots2z@bmi-460g10-05 fastq3]$ humann --input MP00064_Latha_merged.fastq.gz --output MP00064_Latha_merged_output
Creating output directory: /scratch/kots2z/staph_files_neg/fastq3/MP00064_Latha_merged_output
Output files will be written to: /scratch/kots2z/staph_files_neg/fastq3/MP00064_Latha_merged_output
Decompressing gzipped file …
Critical Error: Unable to unzip input file: /scratch/kots2z/staph_files_neg/fastq3/MP00064_Latha_merged.fastq.gz
CRITICAL ERROR: Unable to use gzipped input file. Please check the format of the input file.
(biobakery) [kots2z@bmi-460g10-05 fastq3]$ humann --input 75_NL_1_merged.fastq.gz --output 75_NL_1_merged_output
Creating output directory: /scratch/kots2z/staph_files_neg/fastq3/75_NL_1_merged_output
Output files will be written to: /scratch/kots2z/staph_files_neg/fastq3/75_NL_1_merged_output
Decompressing gzipped file …
Traceback (most recent call last):
File “/usr/local/anaconda3-2020/envs/biobakery/bin/humann”, line 33, in
sys.exit(load_entry_point(‘humann==3.0.0a4’, ‘console_scripts’, ‘humann’)())
File “/usr/local/anaconda3-2020/envs/biobakery/lib/python3.7/site-packages/humann/humann.py”, line 907, in main
check_requirements(args)
File “/usr/local/anaconda3-2020/envs/biobakery/lib/python3.7/site-packages/humann/humann.py”, line 619, in check_requirements
new_file=utilities.gunzip_file(args.input)
File “/usr/local/anaconda3-2020/envs/biobakery/lib/python3.7/site-packages/humann/utilities.py”, line 250, in gunzip_file
shutil.copyfileobj(file_handle_gzip, file_handle)
File “/usr/local/anaconda3-2020/envs/biobakery/lib/python3.7/shutil.py”, line 79, in copyfileobj
buf = fsrc.read(length)
File “/usr/local/anaconda3-2020/envs/biobakery/lib/python3.7/gzip.py”, line 300, in read1
return self._buffer.read1(size)
File “/usr/local/anaconda3-2020/envs/biobakery/lib/python3.7/_compression.py”, line 68, in readinto
data = self.read(len(byte_view))
File “/usr/local/anaconda3-2020/envs/biobakery/lib/python3.7/gzip.py”, line 482, in read
uncompress = self._decompressor.decompress(buf, size)
zlib.error: Error -3 while decompressing data: invalid distance too far back