"You Have 0 Sequences" Error When Running pipits_funits

[brycealex]

I've been receiving the following error while running pipits_funits on the test data set:

2018-09-18 09:13:01 pipits_funits started 2018-09-18 09:13:01 Checking input FASTA for illegal characters 2018-09-18 09:13:01 ... done 2018-09-18 09:13:01 Counting input sequences 2018-09-18 09:13:01 ... number of input sequences: 7394 2018-09-18 09:13:01 Dereplicating sequences for efficiency 2018-09-18 09:13:01 ... done 2018-09-18 09:13:01 Counting dereplicated sequences 2018-09-18 09:13:01 ... number of dereplicated sequences: 3488 2018-09-18 09:13:01 Extracting ITS2 from sequences [ITSx] 2018-09-18 09:40:19 ... done 2018-09-18 09:40:19 Counting ITS sequences (dereplicated) 2018-09-18 09:40:19 ERROR: You have 0 sequences!

Could you help me with this?

[hsgweon]

@boojawaj123 Can you attach the log file?

[brycealex]

^[[91m2018-09-18 09:13:01^[[0m pipits_funits started ^[[91m2018-09-18 09:13:01^[[0m ^[[0mChecking input FASTA for illegal characters^[[0m ^[[91m2018-09-18 09:13:01^[[0m ^[[94m... done^[[0m ^[[91m2018-09-18 09:13:01^[[0m ^[[0mCounting input sequences^[[0m ^[[91m2018-09-18 09:13:01^[[0m ^[[94m... number of input sequences: 7394^[[0m ^[[91m2018-09-18 09:13:01^[[0m ^[[0mDereplicating sequences for efficiency^[[0m vsearch v2.8.3_linux_x86_64, 1007.8GB RAM, 72 cores https://github.com/torognes/vsearch

Dereplicating file out_seqprep/prepped.fasta 100% 1961564 nt in 7394 seqs, min 111, max 430, avg 265 Sorting 100% 3488 unique sequences, avg cluster 2.1, median 1, max 179 Writing output file 100% Writing uc file, first part 100% Writing uc file, second part 100% ^[[91m2018-09-18 09:13:01^[[0m ^[[94m... done^[[0m ^[[91m2018-09-18 09:13:01^[[0m ^[[0mCounting dereplicated sequences^[[0m ^[[91m2018-09-18 09:13:01^[[0m ^[[94m... number of dereplicated sequences: 3488^[[0m ^[[91m2018-09-18 09:13:01^[[0m ^[[0mExtracting ITS2 from sequences [ITSx]^[[0m ITSx -- Identifies ITS sequences and extracts the ITS region by Johan Bengtsson-Palme et al., University of Gothenburg Version: 1.1b1

Tue Sep 18 09:13:01 2018 : Preparing HMM database (should be quick)... Tue Sep 18 09:13:01 2018 : Checking and handling input sequence data (should not take long)... Tue Sep 18 09:13:02 2018 : Comparing sequences to HMM database (this may take a long while)... Tue Sep 18 09:27:12 2018 : Fungi analysis of main strand finished. Tue Sep 18 09:40:19 2018 : Fungi analysis of complementary strand finished. Tue Sep 18 09:40:19 2018 : Analysing results of HMM-scan (this might take quite some time)... Tue Sep 18 09:40:19 2018 : Extraction finished!

Thank you for using ITSx! Please report bugs or unsupported lineages to itsx@microbiology.se

^[[91m2018-09-18 09:40:19^[[0m ^[[94m... done^[[0m ^[[91m2018-09-18 09:40:19^[[0m ^[[0mCounting ITS sequences (dereplicated)^[[0m ^[[91m2018-09-18 09:40:19^[[0m ^[[91mERROR: You have 0 sequences!^[[0m

[hsgweon]

And your input command?

[brycealex]

pipits_funits -i out_seqprep/prepped.fasta -o out_funits -x ITS2

[hsgweon]

Hmm... this is new. Surprised to see that it took 27 minutes to run the test data. What spec is your machine? and which OS are you running it on? Ubuntu? macOS?

Also can you try:

conda install vsearch=2.8.0 -y

and then run

pipits_funits -i out_seqprep/prepped.fasta -o out_funits -x ITS2

[brycealex]

I received the same error unfortunately. I'm running on Ubuntu, accessing a remote server.

Here are the specs of the server:

Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 72 On-line CPU(s) list: 0-71 Thread(s) per core: 2 Core(s) per socket: 18 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family: 6 Model: 79 Model name: Intel(R) Xeon(R) CPU E5-2697 v4 @ 2.30GHz Stepping: 1 CPU MHz: 1216.574 CPU max MHz: 3600.0000 CPU min MHz: 1200.0000 BogoMIPS: 4601.18 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 46080K NUMA node0 CPU(s): 0-17,36-53 NUMA node1 CPU(s): 18-35,54-71

[brycealex]

I believe I was running the previous commands incorrectly, but I figured it out. Thank you for your help.

[hsgweon]

Can you let me know what the problem was and how you solved it?