AttributeError: 'NoneType' object has no attribute 'dumps'

[JoyLiu19]

Hi, Professor Zhou, I have installed PEPPAN following the instructions on GitHub. However, I encountered an error while running the example files. The error message is as follows:

FileNotFoundError: AttributeError: 'NoneType' object has no attribute 'dumps'

Could you please help me solve this issue? Thank you. Here is the full code that I ran:

(PEPPAN) liujiayu@JoyBook ~ % PEPPAN -p examples/ST131 examples/*.gff.gz 2023-04-27 15:55:33.475374 COMMAND: /Users/liujiayu/miniconda3/bin/PEPPAN -p examples/ST131 examples/GCF_000010485.combined.gff.gz examples/GCF_000214765.combined.gff.gz examples/GCF_001566635.combined.gff.gz examples/GCF_001577325.combined.gff.gz 2023-04-27 15:56:01.257752 Run MMSeqs linclust to get exemplar sequences. Params: 0.9 identities and 0.8 align ratio ./NS_scaigasw/tmp/18279923315520868573/linclust.sh: line 37: 51013 Segmentation fault: 11 "$MMSEQS" clust "$INPUT" "${TMP_PATH}/pref_rescore1" "${TMP_PATH}/pre_clust" ${CLUSTER_PAR} No datafile could be found for ./NS_scaigasw/seq.lc! Traceback (most recent call last): File "/Users/liujiayu/miniconda3/bin/PEPPAN", line 8, in sys.exit(ortho()) File "/Users/liujiayu/miniconda3/lib/python3.9/site-packages/PEPPAN/PEPPAN.py", line 1884, in ortho params['clust'] = iterClust(params['prefix'], params['genes'], groups, dict(identity=params['clust_identity'], coverage=params['clust_match_prop'], n_thread=params['n_thread'], translate=False)) File "/Users/liujiayu/miniconda3/lib/python3.9/site-packages/PEPPAN/PEPPAN.py", line 1784, in iterClust g, clust = getClust(prefix, g, params) File "/Users/liujiayu/miniconda3/lib/python3.9/site-packages/PEPPAN/modules/clust.py", line 67, in getClust with open(tabFile) as fin : FileNotFoundError: [Errno 2] No such file or directory: './NS_scaigasw/clust.tab' Exception ignored in: <function Pool.del at 0x7fb1892701f0> Traceback (most recent call last): File "/Users/liujiayu/miniconda3/lib/python3.9/multiprocessing/pool.py", line 268, in del File "/Users/liujiayu/miniconda3/lib/python3.9/multiprocessing/queues.py", line 372, in put AttributeError: 'NoneType' object has no attribute 'dumps' Exception ignored in: <function Pool.del at 0x7fb1892701f0> Traceback (most recent call last): File "/Users/liujiayu/miniconda3/lib/python3.9/multiprocessing/pool.py", line 268, in del File "/Users/liujiayu/miniconda3/lib/python3.9/multiprocessing/queues.py", line 372, in put AttributeError: 'NoneType' object has no attribute 'dumps'

Thank you for your help. Best regards, Joy Liu