search

PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
249 stars 44 forks source link

BAM2fastx tools not working #559

Closed salvatierra8 closed 1 year ago

salvatierra8 commented 1 year ago

Operating system Ubuntu 22.04.1 LTS

Package name BAM2fastx tools

Conda environment packages in environment at /home/salvatierra/anaconda3/envs/converters_env:

Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge bam2fastx 1.3.1 hb7da652_2 bioconda bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2022.12.7 ha878542_0 conda-forge htslib 1.16 h6bc39ce_0 bioconda keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.20.1 hf9c8cef_0 conda-forge libcurl 7.87.0 h6312ad2_0 conda-forge libdeflate 1.13 h166bdaf_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libnghttp2 1.51.0 hdcd2b5c_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge ncurses 6.3 h27087fc_1 conda-forge openssl 1.1.1s h0b41bf4_1 conda-forge pbbam 2.1.0 h218f6fc_3 bioconda pbcopper 2.0.0 ha04c180_1 bioconda pbtk 1.0.0 h9ee0642_0 bioconda xz 5.2.6 h166bdaf_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge

Error message

|> 20230114 16:47:04.209 -|- FATAL -|- Run -|- 0x7fa27e0be3c0|| -|- bam2fastq ERROR: [pbbam] PBI index I/O ERROR: could not open file for reading: file: /home/salvatierra/Downloads/H1_1_m64168e_220404_060128.subreads-002.bam.pbi reason: No such file or directory

Describe the issue/bug(?) I'm a fresh new user for ubuntu, conda, ngs analysis and any other dependencies for the matter, please have patience. All i understand right now is that i need bam2fastx tool to convert my reads into fastq or fasta in order to assembly em using masurca, there's some error during the process and it's related to the pacbio reads, as another companion and me have to do something similar both used samtools to convert to fasta. I began theorizing that something must be exclusive to the conversion process after trying to analyze the raw reads through bioconductor, i found out that there's no support to do this, and even more someone mentioned in an issue at github that pb data must be analyzed with pb tools to properly convert data obtained from this instruments. So i followed what the github says, and all i get is a file with the name used of 20 bytes, along an error. I do not know what's going on, could be this python 2.7 thing, or maybe a dependency which is not mentioned in the page (like this pbindex which now seems to be pbbam)

Might or might not be important: If i go to another directory where the bam file is not present and use the command i'll get the same 20 b file in the new directory. So the command is not actually using the file, so this must be related to what "reason:" points out

To Reproduce bam2fastq -o pacbioseq H1_1_m64168e_220404_060128.subreads-002.bam

Expected behavior fastq file corresponding to original bam file

armintoepfer commented 1 year ago

For your use-case, use samtools fasta. It's much simpler and sufficient for what you are trying to achieve.

salvatierra8 commented 1 year ago

For anyone using this tool and happens to get a similar error, checksum your file, problem could be related to an unknown issue after downloading the file, as it pointed out that it was unable to authenticate the file's content. So I just redownload everything again, checksum was ok, and the tool worked.