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donia-lab / MetaBGC

A metagenomic strategy for harnessing the chemical repertoire of the human microbiome
GNU General Public License v3.0
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metabgc search suddenly stops #20

Open aimirza opened 3 years ago

aimirza commented 3 years ago

After running metabgc search my job ended with the following last std outputs. I don't see the file identified-biosynthetic-reads.fasta file anywhere (the expected file generated from metabgc identify). I don't think it rand quantifyand cluster. 

HMMER searching exiting for: /home/amirza/MetaBGC/MetaBGC/Models/Cyclase_TcmJ/Cyclase_TcmJ__30_10__90_120.hmm
Metabgc-identify HMMER search is complete.
Starting extract in: 39 sample files.
Setting up consumers.
Starting up consumer sub-processes.

My code is:

metabgc search --sphmm_directory /home/amirza/MetaBGC/MetaBGC/Models/Cyclase_TcmJ/ --nucl_seq_directory ~/biobakery/kneaddata/final/ --seq_fmt FASTQ --pair_fmt split --r1_file_suffix repeats.removed.all.1.fastq --r2_file_suffix repeats.removed.all.2.fastq --prot_family_name Cyclase_TcmJ--cohort_name TcmJ --output_directory /home/amirza/MetaBGC/TcmJ --cpu 16

8 GB memory (RAM) was allocated to each core.

niki1111 commented 7 months ago

issues.docx AttributeError: 'DataFrame' object has no attribute 'append'

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