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linnarsson-lab / loompy

Python implementation of the Loom file format - http://loompy.org
BSD 2-Clause "Simplified" License
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"AttributeError: 'list' object has no attribute 'shape'" in saving loom file using loompy fromfq #137

Closed Malindrie closed 3 years ago

Malindrie commented 3 years ago

Hello,

I used the loompy command line tool to create a loom file from fastqs. Everything runs well until the save loom file step. I get the error "AttributeError: 'list' object has no attribute 'shape'". Any help with this is much appreciated. Below I have copied the output I get.

2020-10-07 07:24:44,050 - INFO - [index] k-mer length: 31 2020-10-07 07:24:44,050 - INFO - [index] number of targets: 845,338 2020-10-07 07:24:44,051 - INFO - [index] number of k-mers: 271,648,279 2020-10-07 07:25:18,395 - INFO - [index] number of equivalence classes: 4,776,424 2020-10-07 07:25:37,539 - INFO - [quant] will process sample 1: /QRISdata/Q3112/seq_data/WOLV-0001/cellranger/fastq/combined/A3_d40/A3_d40_S2_L001_R1_001.fastq.gz 2020-10-07 07:25:37,539 - INFO - /QRISdata/Q3112/seq_data/WOLV-0001/cellranger/fastq/combined/A3_d40/A3_d40_S2_L001_R2_001.fastq.gz 2020-10-07 07:25:37,539 - INFO - [quant] will process sample 2: /QRISdata/Q3112/seq_data/WOLV-0001/cellranger/fastq/combined/A3_d40/A3_d40_S2_L002_R1_001.fastq.gz 2020-10-07 07:25:37,539 - INFO - /QRISdata/Q3112/seq_data/WOLV-0001/cellranger/fastq/combined/A3_d40/A3_d40_S2_L002_R2_001.fastq.gz 2020-10-07 07:25:37,539 - INFO - [quant] will process sample 3: /QRISdata/Q3112/seq_data/WOLV-0001/cellranger/fastq/combined/A3_d40/A3_d40_S2_L003_R1_001.fastq.gz 2020-10-07 07:25:37,539 - INFO - /QRISdata/Q3112/seq_data/WOLV-0001/cellranger/fastq/combined/A3_d40/A3_d40_S2_L003_R2_001.fastq.gz 2020-10-07 07:25:37,540 - INFO - [quant] will process sample 4: /QRISdata/Q3112/seq_data/WOLV-0001/cellranger/fastq/combined/A3_d40/A3_d40_S2_L004_R1_001.fastq.gz 2020-10-07 07:25:37,540 - INFO - /QRISdata/Q3112/seq_data/WOLV-0001/cellranger/fastq/combined/A3_d40/A3_d40_S2_L004_R2_001.fastq.gz 2020-10-07 07:32:44,594 - INFO - [quant] finding pseudoalignments for the reads ... done 2020-10-07 07:32:44,595 - INFO - [quant] processed 188,630,497 reads, 134,736,788 reads pseudoaligned 2020-10-07 07:33:00,865 - INFO - Loading gene metadata 2020-10-07 07:33:01,452 - INFO - Loading fragments-to-gene mappings 2020-10-07 07:33:02,204 - INFO - Indexing genes 2020-10-07 07:33:02,689 - INFO - Loading equivalence classes 2020-10-07 07:33:39,213 - INFO - Mapping equivalence classes to genes 2020-10-07 07:33:54,288 - INFO - Loading fragment IDs 2020-10-07 07:33:54,609 - INFO - Loading BUS records 2020-10-07 07:38:05,403 - INFO - Sorting cell IDs 2020-10-07 07:38:13,811 - INFO - Found 134,736,788 records for 60,662 genes and 1,831,180 uncorrected cell barcodes. 2020-10-07 07:38:13,812 - INFO - Correcting cell barcodes 2020-10-07 07:43:14,571 - INFO - Found 488,409 corrected cell barcodes. 2020-10-07 07:43:14,572 - INFO - Removing redundant reads using UMIs 2020-10-07 07:45:35,084 - INFO - 51% sequencing saturation. 2020-10-07 07:45:35,085 - INFO - Counting pseudoalignments for main matrix 2020-10-07 07:46:13,002 - INFO - Found 33,990,938 UMIs. 2020-10-07 07:46:13,964 - INFO - Counting pseudoalignments for layer 'unspliced' 2020-10-07 07:50:35,962 - INFO - Found 15,647,623 UMIs. 2020-10-07 07:50:36,665 - INFO - Counting pseudoalignments for layer 'spliced' 2020-10-07 07:55:53,793 - INFO - Found 21,902,684 UMIs. 2020-10-07 07:55:53,793 - INFO - Calling cells 2020-10-07 07:59:21,991 - INFO - Found 12782 valid cells and ~6281 ambient UMIs. 2020-10-07 07:59:21,991 - INFO - Creating loom file 'DWSY.loom' 2020-10-07 07:59:21,991 - INFO - Saving Traceback (most recent call last): File "/home/s4566105/miniconda3/envs/r_newenv/bin/loompy", line 8, in sys.exit(cli()) File "/home/s4566105/miniconda3/envs/r_newenv/lib/python3.7/site-packages/click/core.py", line 829, in call return self.main(args, kwargs) File "/home/s4566105/miniconda3/envs/r_newenv/lib/python3.7/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/home/s4566105/miniconda3/envs/r_newenv/lib/python3.7/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/s4566105/miniconda3/envs/r_newenv/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/s4566105/miniconda3/envs/r_newenv/lib/python3.7/site-packages/click/core.py", line 610, in invoke return callback(args, **kwargs) File "/home/s4566105/miniconda3/envs/r_newenv/lib/python3.7/site-packages/loompy/commands.py", line 34, in fromfq create_from_fastq(loomfile, sampleid, list(fastqs), indexdir, metadatafile, threads) File "/home/s4566105/miniconda3/envs/r_newenv/lib/python3.7/site-packages/loompy/bus_file.py", line 455, in create_from_fastq bus.save(out_file, sample_id, samples_metadata_file) File "/home/s4566105/miniconda3/envs/r_newenv/lib/python3.7/site-packages/loompy/bus_file.py", line 350, in save create(out_file, layers, row_attrs, col_attrs, file_attrs=global_attrs) File "/home/s4566105/miniconda3/envs/r_newenv/lib/python3.7/site-packages/loompy/loompy.py", line 985, in create if ra.shape[0] != shape[0]: AttributeError: 'list' object has no attribute 'shape'

slinnarsson commented 3 years ago

I think I've fixed the bug now. Pull the latest version and see if it works.