All sequences are low abundance (<10X)

[daicy527]

on which platform/server? (Windows? Windows Sublinux? MacOS? Ubuntu? etc.)

Ubuntu

MitoZ version?

3.6

How did you install MitoZ? (e.g. Docker, Udocker, Singularity, Conda-Pack, Conda, or source code)

conda

Did you run a test after your installation, and was the test run okay?

The run on the test data showed this information: "All sequences are low abundance (<10X)"

How much data (roughly) did you use for mitogenome assembly? e.g. 5Gbp?

The command you used?

Problem description

Log messages from MitoZ (stdout and stderr, e.g., both m.log and m.err files)

2025-12-10 11:36:05,127 - mitoz.utility.utility - WARNING -
filter_by_abundance():
All sequences are low abundance (<10X)

[linzhi2013]

Did you see something like:

NCBI database not present yet (first time used?)
Traceback (most recent call last):
  File "/gpfs/hpc/home/kib_unit/XXX/database/mitoz3.6/lib/python3.8/urllib/request.py", line 1354, in do_open
    h.request(req.get_method(), req.selector, req.data, headers,
  File "/gpfs/hpc/home/kib_unit/XXX/database/mitoz3.6/lib/python3.8/http/client.py", line 1256, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/gpfs/hpc/home/kib_unit/XXX/database/mitoz3.6/lib/python3.8/http/client.py", line 1302, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/gpfs/hpc/home/kib_unit/XXX/database/mitoz3.6/lib/python3.8/http/client.py", line 1251, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/gpfs/hpc/home/kib_unit/XXX/database/mitoz3.6/lib/python3.8/http/client.py", line 1011, in _send_output
    self.send(msg)
  File "/gpfs/hpc/home/kib_unit/XXX/database/mitoz3.6/lib/python3.8/http/client.py", line 951, in send
    self.connect()
  File "/gpfs/hpc/home/kib_unit/XXX/database/mitoz3.6/lib/python3.8/http/client.py", line 1418, in connect
    super().connect()
  File "/gpfs/hpc/home/kib_unit/XXX/database/mitoz3.6/lib/python3.8/http/client.py", line 922, in connect
    self.sock = self._create_connection(
  File "/gpfs/hpc/home/kib_unit/XXX/database/mitoz3.6/lib/python3.8/socket.py", line 787, in create_connection
    for res in getaddrinfo(host, port, 0, SOCK_STREAM):
  File "/gpfs/hpc/home/kib_unit/XXX/database/mitoz3.6/lib/python3.8/socket.py", line 918, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -2] Name or service not known

This indicates the Etetoolkit database was not installed properly. You can download and install it manually.

Please refer to

• https://github.com/linzhi2013/MitoZ/wiki/Installation#71-installation-of-the-etetoolkit-database