Error can not find pipits_uc2otutable in line 35, in <module>

[luongphekidz07]

Hi I am using pipits_process with the command:

pipits_process -i /hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_funits6/ITS.fasta -o /hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_process6

However, I received the errors as below:

pipits_process 2.8, the PIPITS Project https://github.com/hsgweon/pipits

2022-09-01 18:45:46 pipits_process started 2022-09-01 18:45:46 Generating a sample list from the input sequences 2022-09-01 18:46:04 Downloading UNITE trained database, version: 10.05.2021 2022-09-01 18:46:05 ... DB directory and files exits, and all looking good. No need to download. 2022-09-01 18:46:05 ... Unpacking 2022-09-01 18:46:10 ... done 2022-09-01 18:46:10 Downloading WARCUP trained database: 2022-09-01 18:46:10 ... DB directory and files exits, and all looking good. No need to download. 2022-09-01 18:46:10 ... Unpacking 2022-09-01 18:46:11 ... done 2022-09-01 18:46:11 Downloading UCHIME database for chimera filtering: 2022-09-01 18:46:11 ... DB directory and files exits, and all looking good. No need to download. 2022-09-01 18:46:11 ... Unpacking 2022-09-01 18:46:11 ... done 2022-09-01 18:46:11 Dereplicating and removing unique sequences prior to picking OTUs vsearch v2.18.0_linux_x86_64, 7.6GB RAM, 2 cores https://github.com/torognes/vsearch

Dereplicating file /hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_funits6/ITS.fasta 100% 1618981758 nt in 8399800 seqs, min 100, max 462, avg 193 Sorting 100% 429233 unique sequences, avg cluster 19.6, median 1, max 732858 Writing output file 100% 68158 uniques written, 361075 clusters discarded (84.1%) 2022-09-01 18:46:21 Picking OTUs [VSEARCH] vsearch v2.18.0_linux_x86_64, 7.6GB RAM, 2 cores https://github.com/torognes/vsearch

Reading file /hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_process6/intermediate/input_nr.fasta 100% 13560288 nt in 68158 seqs, min 102, max 372, avg 199 Masking 100% Sorting by length 100% Counting k-mers 100% Clustering 100% Sorting clusters 100% Writing clusters 100% Clusters: 1319 Size min 1, max 6769, avg 51.7 Singletons: 458, 0.7% of seqs, 34.7% of clusters 2022-09-01 18:46:33 Removing chimeras [VSEARCH] vsearch v2.18.0_linux_x86_64, 7.6GB RAM, 2 cores https://github.com/torognes/vsearch

Reading file pipits_db/uchime_reference_dataset_28.06.2017/uchime_reference_dataset_28.06.2017.fasta 100% 16786547 nt in 30555 seqs, min 146, max 2570, avg 549 Masking 100% Counting k-mers 100% Creating k-mer index 100% Detecting chimeras 100% Found 519 (39.3%) chimeras, 792 (60.0%) non-chimeras, and 8 (0.6%) borderline sequences in 1319 unique sequences. Taking abundance information into account, this corresponds to 12389 (2.1%) chimeras, 584070 (97.8%) non-chimeras, and 453 (0.1%) borderline sequences in 596912 total sequences. 2022-09-01 18:46:37 Renaming OTUs 2022-09-01 18:46:37 Mapping reads onto centroids [VSEARCH] vsearch v2.18.0_linux_x86_64, 7.6GB RAM, 2 cores https://github.com/torognes/vsearch

Reading file /hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_process6/intermediate/input_nr_otus_nonchimeras_relabelled.fasta 100% 147858 nt in 792 seqs, min 102, max 372, avg 187 Masking 100% Counting k-mers 100% Creating k-mer index 100% Searching 100% Matching unique query sequences: 8307353 of 8399800 (98.90%) 2022-09-01 19:04:23 Making OTU table Traceback (most recent call last): File "/hpc/home/nguyenl15/.conda/envs/pipits_env/bin/pipits_uc2otutable", line 35, in infile = open(options.infile, "r") FileNotFoundError: [Errno 2] No such file or directory: '/hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_process6/intermediate/otus.uc' 2022-09-01 19:04:23 Error: None zero returncode: python /hpc/home/nguyenl15/.conda/envs/pipits_env/bin/pipits_uc2otutable -i /hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_process6/intermediate/otus.uc -o /hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_process6/intermediate/otu_table_prelim.txt -l /hpc/home/nguyenl15/Phuong_ITS/ITS_FCG_out_process6/sampleIDs.txt

Could you give some advice?

Thank you, Kind regards, Le Phuong Nguyen