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3DGenomes / TADbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
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tadbit map ValueError #344

Closed eng3001 closed 3 years ago

eng3001 commented 3 years ago

I conda installed TADbit using the directions on your website and have been trying to run tadbit map and have been continuously running into the following error: ValueError: file has no sequences defined (mode='r') - is it SAM/BAM format? Consider opening with check_sq=False

Commands used: tadbit map -w MAP_DIR --fastq s_obliquus_S3HiC_R1_clean.fastq --index assembly.fasta --read 1 --cpus 6 --renz Sau3AI tadbit map -w MAP_DIR --fastq s_obliquus_S3HiC_R2_clean.fastq --index assembly.fasta --read 2 --cpus 6 --renz Sau3AI tadbit map -w DUAL_MAP_DIR --fastq s_obliquus_S3HiC_R2_clean.fastq --fastq2 s_obliquus_S3HiC_R2_clean.fastq --genome GENOME --index assembly.fasta --read 0 --cpus 6 --renz Sau3AI

TADbit output: Writing versions of TADbit and dependencies Generating Hi-C QC plot

Any information on how to get around this error would be extremely helpful. Thank you!

david-castillo commented 3 years ago

Hi,

This is correct

tadbit map -w MAP_DIR --fastq s_obliquus_S3HiC_R1_clean.fastq --index assembly.fasta --read 1 --cpus 6 --renz Sau3AI

However for --index you have to use the gem (or bowtie2, hisat2) index not the fasta. In the case of gem you have to use the gem-indexer command line but every mapper has its own indexer.

Regards

David

eng3001 commented 3 years ago

Thank you for the help! Best, Wyatt

eng3001 commented 3 years ago

I have tried building an index for the genome using bowtie2 and hisat2 using the fallowing commands: hisat2-build --threads 24 assembly.fasta S_obliquus bowtie2-build assembly.fasta Scenedesmus_obliquus

I then tried to feed the index builder output path to tadbit map but continue to get the same error. Tadbit map command: /usr/bin/time -v tadbit map -w MAP_DIR --fastq s_obliquus_S3HiC_R1_clean.fastq --index HiSat2_Index --read 1 --cpus 6 --renz Sau3AI /usr/bin/time -v tadbit map -w MAP_DIR --fastq s_obliquus_S3HiC_R2_clean.fastq --index HiSat2_Index --read 2 --cpus 6 --renz Sau3AI

tadbit map --index seems to be searching for an actual .index file in those directories. I will try to use gem-indexer.

david-castillo commented 3 years ago

I guess HiSat2_Index is the folder, you have to put it this way:

--index HiSat2_Index/S_obliquus

eng3001 commented 3 years ago

Command: tadbit map -w MAP_DIR --fastq s_obliquus_S3HiC_R1_clean.fastq --index HiSat2_Index/S_obliquus --read 1 --cpus 6 --renz Sau3AI

Error:

Traceback (most recent call last):
  File "/home/wyatte/.conda/envs/tadbit/bin/tadbit", line 152, in <module>
    main(sys.argv)
  File "/home/wyatte/.conda/envs/tadbit/bin/tadbit", line 149, in main
    args.func(args)
  File "/home/wyatte/.conda/envs/tadbit/lib/python3.7/site-packages/pytadbit/tools/tadbit_map.py", line 47, in run
    check_options(opts)
  File "/home/wyatte/.conda/envs/tadbit/lib/python3.7/site-packages/pytadbit/tools/tadbit_map.py", line 228, in check_options
    raise IOError('ERROR: index file not found at ' + opts.index)
OSError: ERROR: index file not found at HiSat2_Index/S_obliquus

I still get the following error when trying to pass the index into tadbit map.

fransua commented 3 years ago

Hi, Hisat2 does not want a folder, but a truncated file name... For example, on my computer I have these files when building the index:

Homo_sapiens-GRCh38.p13.ht2.1.ht2
Homo_sapiens-GRCh38.p13.ht2.2.ht2
Homo_sapiens-GRCh38.p13.ht2.3.ht2
Homo_sapiens-GRCh38.p13.ht2.4.ht2
Homo_sapiens-GRCh38.p13.ht2.5.ht2
Homo_sapiens-GRCh38.p13.ht2.6.ht2
Homo_sapiens-GRCh38.p13.ht2.7.ht2
Homo_sapiens-GRCh38.p13.ht2.8.ht2

and to work with this, I pass to TADbit: --index Homo_sapiens-GRCh38.p13.ht2

eng3001 commented 3 years ago

Hello, Thank you for the help. I have hisat2 files named:

S_obliquus.1.ht2
S_obliquus.2.ht2
S_obliquus.3.ht2
S_obliquus.4.ht2
S_obliquus.5.ht2
S_obliquus.6.ht2
S_obliquus.7.ht2
S_obliquus.8.ht2

and tried --index HiSat2_Index/S_obliquus.ht2 and am still running into the following error: OSError: ERROR: index file not found at HiSat2_Index/S_obliquus.ht2

fransua commented 3 years ago

Ok, than I understand it should be --index HiSat2_Index/S_obliquus as you tried before... Can you try the same command adding --mapper hisat2 --index HiSat2_Index/S_obliquus

eng3001 commented 3 years ago

Thank you all for the help! --mapper hisat2 --index HiSat2_Index/S_obliquus ran successfully.