Beginning AltAnalyze Analysis... Format: non-log
AltAnalyze version 2.1.3 - Expression Analysis Parameters Being Used...
	database: EnsMart72
	species: Mm
	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: non-log
	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
Number of threads = 4
Using AltDatabase/kallisto/0.43.1/PC/bin/kallisto.exe
Building kallisto index file...
Running kallisto on: Lsk.4 ... kallisto failed due to an unknown error (report to altanalyze.org help).
Traceback (most recent call last):
  File "RNASeq.pyc", line 5182, in runKallisto
  File "RNASeq.pyc", line 5308, in importTPMs
IOError: [Errno 2] No such file or directory: u'C:/Users/GBardai/Desktop/Scratch/FASTQ-GSE70245-DownSampled///ExpressionInput/kallisto/Lsk.4/abundance.tsv'