--- Load OGs with min 0 species from oma /ref/marker_genes - mode = marker_genes ---

Loading files for pre-filter:   0%|          | 28/14877 [00:00<00:53, 279.93 OGsLoading files for pre-filter:   0%|          | 72/14877 [00:00<00:39, 373.51 OGsLoading files for pre-filter:   1%|          | 152/14877 [00:00<00:26, 546.74 OGLoading files for pre-filter:   2%|▏         | 233/14877 [00:00<00:23, 635.72 OGLoading files for pre-filter:   2%|▏         | 327/14877 [00:00<00:19, 742.29 OGLoading files for pre-Loading files for pre-filter: 100%|██████████| 14877/14877 [00:04<00:00, 3183.82 OGs/s]

2024-04-02 06:22:08,327 - read2tree.OGSet - INFO - --- Load ogs and find their corresponding DNA seq from /ref/dna_ref.fa ---

2024-04-02 06:22:08,328 - read2tree.OGSet - INFO - Loading dna_ref.fa into memory. This might take a while . . . 

Loading OGs: 100%|██████████| 14877/14877 [00:02<00:00, 4995.31 OGs/s]

2024-04-02 06:22:11,772 - read2tree.OGSet - INFO - : Gathering of DNA seq for 14877 OGs took 2.97900652885437.

--- Generating reference for mapping ---

Loading records: 100%|██████████| 14877/14877 [00:00<00:00, 316479.40 record/s]

2024-04-02 06:22:11,823 - read2tree.ReferenceSet - INFO - : Extracted 1 reference species form 14877 ogs took 0.04769420623779297

--- Alignment of 14877 OGs ---

2024-04-02 06:22:45,017 - read2tree.wrappers.aligners.mafft - WARNING - is MAFFT_BINARIES set correctly: 

multiprocessing.pool.RemoteTraceback: 

"""

Traceback (most recent call last):

  File "/opt/conda/envs/read2tree_env/lib/python3.9/multiprocessing/pool.py", line 125, in worker

    result = (True, func(*args, **kwds))

  File "/opt/conda/envs/read2tree_env/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar

    return list(map(*args))

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/Aligner.py", line 287, in _align_worker

    alignment = mafft_wrapper()

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/wrappers/aligners/mafft.py", line 107, in __call__

    raise WrapperError('Mafft did not compute any alignments. StdErr: {}'.format(error))

read2tree.wrappers.WrapperError: Mafft did not compute any alignments. StdErr: nthread = 0

nthreadpair = 0

nthreadtb = 0

ppenalty_ex = 0

Warning: Only 1 sequence found.

At least 2 sequences should be input!

Only 1 sequence found.

"""



The above exception was the direct cause of the following exception:



Traceback (most recent call last):

  File "/opt/conda/envs/read2tree_env/bin/read2tree", line 4, in <module>

    __import__('pkg_resources').run_script('read2tree==0.1.5', 'read2tree')

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 706, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1555, in run_script

    exec(script_code, namespace, namespace)

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/EGG-INFO/scripts/read2tree", line 16, in <module>

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/main.py", line 291, in main

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/Aligner.py", line 51, in __init__

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/Aligner.py", line 330, in _align

  File "/opt/conda/envs/read2tree_env/lib/python3.9/multiprocessing/pool.py", line 364, in map

    return self._map_async(func, iterable, mapstar, chunksize).get()

  File "/opt/conda/envs/read2tree_env/lib/python3.9/multiprocessing/pool.py", line 771, in get

    raise self._value

read2tree.wrappers.WrapperError: Mafft did not compute any alignments. StdErr: nthread = 0

nthreadpair = 0

nthreadtb = 0

ppenalty_ex = 0

Warning: Only 1 sequence found.

At least 2 sequences should be input!

Only 1 sequence found.

Re-loading files: 0 OGs [00:00, ? OGs/s]--- Re-load ogs and find their corresponding DNA seq from output folder ---

Re-loading files: 14877 OGs [00:01, 8084.23 OGs/s]

--- Generating reference for mapping from folder ---

Re-loading references for mapping from folder: 100%|██████████| 1/1 [00:00<00:00,  4.09 species/s]

--- Alignment of 191 OGs ---

2024-04-02 06:22:53,591 - read2tree.Aligner - INFO - NAPOINLI49_S157_L002_R1_001: Alignment of 191 OGs took 3.3476128578186035.

--- Mapping of reads to reference sequences ---

Mapping reads to species:   0%|          | 0/1 [00:00<?, ? species/s]2024-04-02 06:22:53,626 - read2tree.Mapper - INFO - NAPOINLI49_S157_L002_R1_001: --- Mapping of reads to NAUPO reference species ---

^[[B^[[B^[[B^[[B2024-04-02 06:42:09,836 - read2tree.Mapper - INFO - NAPOINLI49_S157_L002_R1_001: Mapped 948354 / 23514778 reads to NAUPO_OGs.fa

2024-04-02 06:42:09,891 - read2tree.Mapper - INFO - NAPOINLI49_S157_L002_R1_001: Mapping to NAUPO_OGs.fa references took 1156.2387206554413.

Mapping reads to species: 100%|██████████| 1/1 [29:14<00:00, 1754.83s/ species]

Adding mapped seq to alignments: 100%|██████████| 191/191 [00:00<00:00, 572222.90 alignments/s]

Adding mapped seq to OG: 100%|██████████| 191/191 [00:00<00:00, 649199.40 OGs/s]

Adding mapped seq to OG:   0%|          | 0/191 [00:00<?, ? OGs/s]--- Add inferred mapped sequence back to OGs ---

Adding mapped seq to OG: 100%|██████████| 191/191 [00:00<00:00, 29507.98 OGs/s]

2024-04-02 06:52:19,747 - read2tree.OGSet - INFO - NAPOINLI49_S157_L002_R1_001: Appending 11838 reconstructed sequences to present OG took 0.007886886596679688.

--- Add inferred mapped sequence back to alignment ---

Adding mapped seq to alignments: 100%|██████████| 191/191 [00:00<00:00, 455177.31 alignments/s]

2024-04-02 06:52:19,750 - read2tree.Aligner - INFO - NAPOINLI49_S157_L002_R1_001: Appending 0 reconstructed sequences to present Alignments took 0.001127481460571289.

--- Tree inference ---

2024-04-02 06:52:19,897 - read2tree.wrappers.treebuilders.parsers - ERROR - [Errno 2] No such file or directory: '/tmp/iqtree_mo9uflrr/tmp_output.treefile'

[Errno 2] No such file or directory: '/tmp/iqtree_mo9uflrr/tmp_output.treefile'

Traceback (most recent call last):

  File "/opt/conda/envs/read2tree_env/bin/read2tree", line 4, in <module>

    __import__('pkg_resources').run_script('read2tree==0.1.5', 'read2tree')

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 706, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1555, in run_script

    exec(script_code, namespace, namespace)

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/EGG-INFO/scripts/read2tree", line 16, in <module>

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/main.py", line 345, in main

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/TreeInference.py", line 42, in __init__

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/TreeInference.py", line 54, in _infer_tree

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/wrappers/treebuilders/iqtree.py", line 73, in __call__

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/wrappers/treebuilders/iqtree.py", line 118, in _read_result

TypeError: 'NoneType' object is not subscriptable

Re-loading files: 0 OGs [00:00, ? OGs/s]--- Re-load ogs and find their corresponding DNA seq from output folder ---

Re-loading files: 14877 OGs [00:02, 5537.48 OGs/s]

--- Generating reference for mapping from folder ---

Re-loading references for mapping from folder: 100%|██████████| 1/1 [00:00<00:00,  3.69 species/s]

--- Alignment of 191 OGs ---

2024-04-02 06:52:28,942 - read2tree.Aligner - INFO - NAPOINLI31_S156_L002_R1_001: Alignment of 191 OGs took 3.233227491378784.

--- Mapping of reads to reference sequences ---

Mapping reads to species:   0%|          | 0/1 [00:00<?, ? species/s]2024-04-02 06:52:28,973 - read2tree.Mapper - INFO - NAPOINLI31_S156_L002_R1_001: --- Mapping of reads to NAUPO reference species ---

2024-04-02 07:14:20,178 - read2tree.Mapper - INFO - NAPOINLI31_S156_L002_R1_001: Mapped 1202421 / 28999640 reads to NAUPO_OGs.fa

2024-04-02 07:14:20,230 - read2tree.Mapper - INFO - NAPOINLI31_S156_L002_R1_001: Mapping to NAUPO_OGs.fa references took 1311.2357428073883.

Mapping reads to species: 100%|██████████| 1/1 [32:05<00:00, 1925.94s/ species]

Adding mapped seq to alignments: 100%|██████████| 191/191 [00:00<00:00, 609210.70 alignments/s]

Adding mapped seq to OG: 100%|██████████| 191/191 [00:00<00:00, 632789.94 OGs/s]

--- Add inferred mapped sequence back to OGs ---

Adding mapped seq to OG: 100%|██████████| 191/191 [00:00<00:00, 33837.89 OGs/s]

2024-04-02 07:24:45,915 - read2tree.OGSet - INFO - NAPOINLI31_S156_L002_R1_001: Appending 12247 reconstructed sequences to present OG took 0.007348537445068359.

--- Add inferred mapped sequence back to alignment ---

Adding mapped seq to alignments: 100%|██████████| 191/191 [00:00<00:00, 425896.90 alignments/s]

2024-04-02 07:24:45,917 - read2tree.Aligner - INFO - NAPOINLI31_S156_L002_R1_001: Appending 0 reconstructed sequences to present Alignments took 0.001039266586303711.

[Errno 2] No such file or directory: '/tmp/iqtree_ac6ajljb/tmp_output.treefile'

--- Tree inference ---

2024-04-02 07:24:46,063 - read2tree.wrappers.treebuilders.parsers - ERROR - [Errno 2] No such file or directory: '/tmp/iqtree_ac6ajljb/tmp_output.treefile'

Traceback (most recent call last):

  File "/opt/conda/envs/read2tree_env/bin/read2tree", line 4, in <module>

    __import__('pkg_resources').run_script('read2tree==0.1.5', 'read2tree')

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 706, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1555, in run_script

    exec(script_code, namespace, namespace)

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/EGG-INFO/scripts/read2tree", line 16, in <module>

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/main.py", line 345, in main

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/TreeInference.py", line 42, in __init__

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/TreeInference.py", line 54, in _infer_tree

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/wrappers/treebuilders/iqtree.py", line 73, in __call__

  File "/opt/conda/envs/read2tree_env/lib/python3.9/site-packages/read2tree-0.1.5-py3.9.egg/read2tree/wrappers/treebuilders/iqtree.py", line 118, in _read_result

TypeError: 'NoneType' object is not subscriptable