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adamewing / tldr

Identify and annotate TE-mediated insertions in long-read sequence data
MIT License
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[E::fai_build_core] Format error, unexpected "C" at line 1 #23

Closed malonematt closed 2 years ago

malonematt commented 2 years ago

When running tldr with: tldr-b /path/to/final.bam -r /path/to/Masked_Genome_061021.fa.fai -o 1217normLength -e none --detail_output --extend_consensus 1000 --procs 16

I run into the error from the title after writing the clusters to the pickle, when it is loading the clusters.

Is this an issue of how my indexed reference is formatted? That's my only thought so far.

malonematt commented 2 years ago

This is the format of my ref.fa.fai: CM025008.1 64216774 90 80 81 CM025009.1 74218288 65019664 80 81 CM025010.1 57828929 140165771 80 81 CM025011.1 49614181 198717652 80 81 CM025012.1 49927339 248952101 80 81 CM025013.1 61955777 299503622 80 81 CM025014.1 43216860 362233937 80 81 CM025015.1 57431038 405991098 80 81 CM025016.1 54464365 464140114 80 81 CM025017.1 49825902 519285375 80 81

malonematt commented 2 years ago

Here is a snippet from my log file
Traceback (most recent call last): File "/home1/malonema/.local/bin/tldr", line 2128, in [E::fai_build_core] Format error, unexpected "C" at line 1 [E::fai_build_core] Format error, unexpected "C" at line 1 [E::fai_build_core] Format error, unexpected "C" at line 1 [E::fai_build_core] Format error, unexpected "C" at line 1 [E::fai_build_core] Format error, unexpected "C" at line 1 [E::fai_build_core] Format error, unexpected "C" at line 1 [E::fai_build_core] Format error, unexpected "C" at line 1 main(args) File "/home1/malonema/.local/bin/tldr", line 1907, in main [E::fai_build_core] Format error, unexpected "C" at line 1 processed_clusters.append(res.get()) File "/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.9.2-uvcroioc4witkp6qf7mbebof5ix4wlb6/lib/python3.9/multiprocessing/pool.py", line 771, in get [E::fai_build_core] Format error, unexpected "C" at line 1 [E::fai_build_core] Format error, unexpected "C" at line 1 raise self._value OSError: error when opening file /project/bbenayou_34/malone/nanopore/Masked_Genome_061021.fa.fai [E::fai_build_core] Format error, unexpected "C" at line 1 [E::fai_build_core] Format error, unexpected "C" at line 1

adamewing commented 2 years ago

You're feeding it the index instead of the .fasta, try -r /path/to/Masked_Genome_061021.fa instead and let me know if that helps.

adamewing commented 2 years ago

closing due to likely resolution