tapestry
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johnomics
KeyError: 'depth'
In installed Tapestry in a Conda environment on our HPC and am trying to run :
weave -a /path/M17.racon3.medaka.pilon.fasta -r /path/ancestor.17.nanopore.nanofilt.fastq.gz -t TTAGGG \
-o /path/pilon_rounds/tapestry_output -c 10 -l 5000
But I keep getting the following error :
2025-11-06 15:06:14 WARNING Output directory /path/tapestry_output found, will use existing analysis files if present and up-to-date, but overwrite reports
2025-11-06 15:06:14 INFO Loading genome assembly
2025-11-06 15:06:14 INFO Loaded 53 contigs from /path/M17.racon3.medaka.pilon.fasta
2025-11-06 15:06:14 INFO Ploidy window size set to 100000 based on assembly N50 length 2359087
2025-11-06 15:06:14 INFO Sampling 50 times coverage of 40.0 Mb assembly from >5000bp reads in /path/ancestor.17.nanopore.nanofilt.fastq.gz
0%| | 0/50 [00:00<?, ?it/s]
2%|▏ | 1/50 [00:06<05:23, 6.60s/it]
4%|▍ | 2/50 [00:19<06:47, 8.49s/it]
6%|▌ | 3/50 [00:32<07:41, 9.82s/it]
8%|▊ | 4/50 [00:45<08:16, 10.80s/it]
10%|█ | 5/50 [00:58<08:36, 11.47s/it]
12%|█▏ | 6/50 [01:11<08:46, 11.96s/it]
14%|█▍ | 7/50 [01:24<08:46, 12.25s/it]
16%|█▌ | 8/50 [01:37<08:43, 12.46s/it]
18%|█▊ | 9/50 [01:50<08:37, 12.62s/it]
20%|██ | 10/50 [02:03<08:29, 12.73s/it]
22%|██▏ | 11/50 [02:16<08:18, 12.78s/it]
24%|██▍ | 12/50 [02:29<08:06, 12.79s/it]
26%|██▌ | 13/50 [02:42<07:54, 12.83s/it]
28%|██▊ | 14/50 [02:55<07:42, 12.84s/it]
30%|███ | 15/50 [03:07<07:29, 12.84s/it]
32%|███▏ | 16/50 [03:20<07:15, 12.81s/it]
34%|███▍ | 17/50 [03:30<06:34, 11.94s/it]
2025-11-06 15:09:48 INFO Wrote 89969 reads (671822300 bases, 17 times coverage) to /path/tapestry_output/reads.fastq.gz
2025-11-06 15:09:48 WARNING Only found 17 times coverage in reads longer than 5000, not 50 times; consider reducing minimum read length (-l)
2025-11-06 15:09:48 INFO Aligning reads /path/tapestry_output/reads.fastq.gz to assembly
2025-11-06 15:11:38 INFO Indexing /path/tapestry_output/reads_assembly.bam
2025-11-06 15:11:41 INFO Aligning contigs /path/tapestry_output/assembly.fasta to assembly
2025-11-06 15:11:47 INFO Indexing /path/tapestry_output/contigs_assembly.bam
2025-11-06 15:13:33 INFO Building alignments database /path/tapestry_output/alignments.db
2025-11-06 15:16:12 INFO Loading contig alignments into database
2025-11-06 15:16:14 INFO Loading read alignments into database
2025-11-06 15:16:29 INFO Finding neighbouring alignments
0%| | 0/7158 [00:00<?, ? alignments/s]
14%|█▍ | 1000/7158 [00:09<00:59, 104.15 alignments/s]
28%|██▊ | 2000/7158 [00:20<00:50, 101.18 alignments/s]
42%|████▏ | 3000/7158 [00:29<00:40, 102.99 alignments/s]
56%|█████▌ | 4000/7158 [00:37<00:29, 108.16 alignments/s]
70%|██████▉ | 5000/7158 [01:02<00:30, 71.23 alignments/s]
84%|████████▍ | 6000/7158 [01:11<00:14, 80.54 alignments/s]
98%|█████████▊| 7000/7158 [01:19<00:01, 89.47 alignments/s]
2025-11-06 15:18:03 INFO Processing 53 contigs
Tapestry version 1.0.1
Dependencies
minimap2 2.24-r1122 /home/caroz/mambaforge/envs/tapestry_env/bin/minimap2
samtools 1.15.1 /home/caroz/mambaforge/envs/tapestry_env/bin/samtools
Welcome to Tapestry!
Assembly to validate /path/M17.racon3.medaka.pilon.fasta
Reads to sample from /path/ancestor.17.nanopore.nanofilt.fastq.gz
Coverage to sample 50
Minimum read length 5000
Telomere sequence(s) TTAGGG
Minimum contig alignment 2000
Output directory /path/pilon_rounds/tapestry_output
Processing contigs: 0%| | 0/53 [00:00<?, ? contig/s]multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/caroz/mambaforge/envs/tapestry_env/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2657, in get_loc
return self._engine.get_loc(key)
File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'depth'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/caroz/mambaforge/envs/tapestry_env/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/home/caroz/mambaforge/envs/tapestry_env/lib/python3.6/site-packages/tapestry/contig.py", line 40, in process_contig
contig.process()
File "/home/caroz/mambaforge/envs/tapestry_env/lib/python3.6/site-packages/tapestry/contig.py", line 114, in process
self.median_read_depth = self.median_depth(self.read_depths)
File "/home/caroz/mambaforge/envs/tapestry_env/lib/python3.6/site-packages/tapestry/contig.py", line 152, in median_depth
return depths['depth'].median() if depths is not None else 0
File "/home/caroz/mambaforge/envs/tapestry_env/lib/python3.6/site-packages/pandas/core/frame.py", line 2927, in __getitem__
indexer = self.columns.get_loc(key)
File "/home/caroz/mambaforge/envs/tapestry_env/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2659, in get_loc
return self._engine.get_loc(self._maybe_cast_indexer(key))
File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'depth'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/caroz/mambaforge/envs/tapestry_env/bin/weave", line 45, in <module>
assembly = Assembly(args.assembly, args.reads, args.telomere, args.output, args.cores, args.depth, args.length, args.windowsize, args.forcereadoutput, args.mincontigalignment)
File "/home/caroz/mambaforge/envs/tapestry_env/lib/python3.6/site-packages/tapestry/assembly.py", line 109, in __init__
self.process_contigs()
File "/home/caroz/mambaforge/envs/tapestry_env/lib/python3.6/site-packages/tapestry/assembly.py", line 316, in process_contigs
for contig in tapestry_tqdm(p.imap(process_contig, self.contigs.values()), total=len(self.contigs), desc="Processing contigs"):
File "/home/caroz/mambaforge/envs/tapestry_env/lib/python3.6/site-packages/tqdm-4.7.2-py3.6.egg/tqdm/_tqdm.py", line 594, in __iter__
File "/home/caroz/mambaforge/envs/tapestry_env/lib/python3.6/multiprocessing/pool.py", line 735, in next
raise value
KeyError: 'depth'
I changed the depth to -d 17, but it gave the same error.
