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xuechunxu / DiTing

DiTing: A pipeline to infer and compare biogeochemical pathways in metagenomic data
GNU General Public License v3.0
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When input .fastq.gz files ,it gets wrong #17

Open ArthurKaslen opened 2 years ago

ArthurKaslen commented 2 years ago

-----Here is the wrong code----- 2022-08-19 23:41:23 [INFO ] User input: /home/miniconda3/envs/diting-env/bin/diting.py -r rawdata -o testone -n 120 **[1/12] Check database**** 2022-08-19 23:41:23 [INFO ] The KEGG database is set 2022-08-19 23:41:23 [INFO ] The DMSP database is set 2022-08-19 23:41:23 [INFO ] [2/12] Metagenomic assembly**** 2022-08-19 23:41:23 [INFO ] Megahit Assembly for GZ36_GJ_1.raw 2022-08-19 23:41:23 [INFO ] Metagenomic assembly by MEGAHIT started 2022-08-19 23:41:23 [INFO ] megahit -1 rawdata/GZ36_GJ_1.raw_1.fastq.gz -2 rawdata/GZ36_GJ_1.raw_2.fastq.gz -o testone/assembly_tmp -t 120 2022-08-19 23:41:23 - MEGAHIT v1.2.9 2022-08-19 23:41:23 - Using megahit_core with POPCNT support 2022-08-19 23:41:23 - Convert reads to binary library gzip: /home/rawdata/GZ36_GJ_1.raw_1.fastq.gz: invalid compressed data--crc error

gzip: /home/rawdata/GZ36_GJ_1.raw_1.fastq.gz: invalid compressed data--length error 2022-08-19 23:43:07 - b'INFO sequence/io/sequence_lib.cpp : 75 - Lib 0 (/home/rawdata/GZ36_GJ_1.raw_1.fastq.gz,/home/rawdata/GZ36_GJ_1.raw_2.fastq.gz): pe, 46229166 reads, 150 max length' 2022-08-19 23:43:07 - b'INFO utils/utils.h : 152 - Real: 103.7972\tuser: 72.1272\tsys: 10.2173\tmaxrss: 248000' 2022-08-19 23:43:07 - Error occurs when reading inputs Traceback (most recent call last): File "/home/miniconda3/envs/diting-env/bin/diting.py", line 259, in main() File "/home/miniconda3/envs/diting-env/bin/diting.py", line 109, in main copy(assembly_ori, assembly_tar) File "/home/miniconda3/envs/diting-env/lib/python3.7/shutil.py", line 248, in copy copyfile(src, dst, follow_symlinks=follow_symlinks) File "/home/miniconda3/envs/diting-env/lib/python3.7/shutil.py", line 120, in copyfile with open(src, 'rb') as fsrc: FileNotFoundError: [Errno 2] No such file or directory: 'testone/assembly_tmp/final.contigs.fa'

ArthurKaslen commented 2 years ago

Could you tell me how to solve the problem? Thanks a lot

SilentGene commented 2 years ago

hi @ArthurKaslen ,

It looks like the program had a problem when trying to unzip your fastq.gz file. Could you check the data integrity of the .gz files? A typical scenario is that people have incomplete or corrupted reads files during data transmission. Or you could try unzipping your fastq.gz file manually first and then run the program.

Regards, Heyu

ArthurKaslen commented 2 years ago

okay，thanks