Error running RNASeq analysis with fastq files as input and assigned to groups

[jaydoc]

When running AltAnalyze to process fastq files using Kallisto-splice if I assign groups to the files then AltAnalyze fails with the following error

Traceback (most recent call last): File "AltAnalyze.py", line 8831, in AltAnalyzeSetup(skip_intro) File "AltAnalyze.py", line 5185, in AltAnalyzeSetup apt_location = fl.APTLocation() File "/home/jaydoc/altanalyze-master/UI.py", line 4566, in APTLocation def APTLocation(self): return self._apt_location AttributeError: ExpressionFileLocationData instance has no attribute '_apt_location'

While this happens immediately after the groups are assigned in Ubuntu Linux (source code run with python2 AltAnalyze.py the same error happens with the Windows binary version as well, except that it fails after the comparisons are specified.

I am trying to process 25 samples with paired reads divided into 8 groups (for a total of 28 comparisons) if that helps.

If I do not assign the groups myself and just check the ICGS option then the program runs kallisto and outputs what I assume are (pseudo)bam files.

Any help is much appreciated.

[nsalomonis]

Greetings,

Could you send the full log file, saved to your output directory by AltAnalyze.

As a test, can you try running from the command line as something like:

python AltAnalyze.py --runICGS yes --platform "RNASeq" --species Mm --column_method hopach --rho 0.4 --SamplesDiffering 4 --excludeCellCycle conservative --output "C:/FASTQ_Files/" --expname "Mm_HSCs" --fastq_dir "C:/FASTQ_Files/" --runKallisto yes

It is possible it is Unix compilation issue for Kallisto splice and this or the log file should reveal.

Best, Nathan

On Aug 4, 2022, at 1:16 PM, Nathan Salomonis @.***> wrote:



Best, Nathan

On Aug 4, 2022, at 1:56 AM, jaydoc @.***> wrote:

 When running AltAnalyze to process fastq files using Kallisto-splice if I assign groups to the files then AltAnalyze fails with the following error

Traceback (most recent call last): File "AltAnalyze.py", line 8831, in AltAnalyzeSetup(skip_intro) File "AltAnalyze.py", line 5185, in AltAnalyzeSetup apt_location = fl.APTLocation() File "/home/jaydoc/altanalyze-master/UI.py", line 4566, in APTLocation def APTLocation(self): return self._apt_location AttributeError: ExpressionFileLocationData instance has no attribute '_apt_location'

While this happens immediately after the groups are assigned in Ubuntu Linux (source code run with python AltAnalyze.py the same error happens with the Windows binary version as well, except that it fails after the comparisons are specified.

I am trying to process 25 samples with paired reads divided into 8 groups (for a total of 28 comparisons) if that helps.

If I do not assign the groups myself and just check the ICGS option then the program runs kallisto and outputs what I assume are (pseudo)bam files.

Any help is much appreciated.

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[Junaid13913]

having same issue below -Beginning AltAnalyze Analysis... Format: scaled AltAnalyze version 2.1.4.4 - Expression Analysis Parameters Being Used... database: EnsMart72 species: Hs method: RNASeq manufacturer: RNASeq probability_statistic: moderated t-test constitutive_source: Ensembl dabg_p: 1.0 junction expression threshold: 5.0 exon_exp_threshold: 5.0 gene_exp_threshold: 200.0 exon_rpkm_threshold: 0.5 gene_rpkm_threshold: 1.0 exclude low expressing exons for RPKM: no avg_all_for_ss: yes expression_data_format: scaled include_raw_data: no run_from_scratch: Process RNA-seq reads perform_alt_analysis: yes calculate_gene_expression_using: core Alternative Exon Analysis Parameters Being Used... analysis_method: MultiPath-PSI p_threshold: 0.05 filter_data_types: all alt_exon_fold_variable: 0.1 gene_expression_cutoff: 10.0 remove_intronic_junctions: no avg_all_for_ss: yes permute_p_threshold: 0.05 perform_permutation_analysis: no export_NI_values: yes run_MiDAS: no use_direct_domain_alignments_only: inferred comparison microRNA_prediction_method: any analyze_all_conditions: pairwise filter_for_AS: no run_GOElite: run-immediately Using AltDatabase/kallisto/0.43.1/PC/bin/kallisto.exe Building kallisto index file... Running kallisto on: GS100DA2 ... kallisto failed due to an unknown error (report to altanalyze.org help). Trying without BAM file creation. Re-Building kallisto index file... kallisto failed due to an unknown error (report to altanalyze.org help). Traceback (most recent call last): File "RNASeq.pyc", line 5286, in runKallisto File "RNASeq.pyc", line 5412, in importTPMs IOError: [Errno 2] No such file or directory: u'E:/project_4///ExpressionInput/kallisto/GS100DA2/abundance.tsv'