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MassTRIX: Mass TRanslator into Pathways

This is MassTRIX reloaded, the 3rd version of MassTRIX.

The jobs on the old server remain still available at this link.
Should you encounter any unexpected behaviour, please let us know!

JobID: EXAMPLE_human

***  human highlight genes  ***

hsa Homo sapiens (human)

  Pathways  |  Compounds  |  Downloads  |  Error plot  |  Log file  |  Input data  
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+ tmp1=eraseme.21554.tmp1
+ tmp2=eraseme.21554.tmp2
+ tmp3=eraseme.21554.tmp3
+ affychiptype=undef
+ foldChange=0.5
+ foldcolorup=red
+ foldcolordown=blue
+ foldcolornorm=no
+ checkbox_natrium=undef
+ checkbox_potassium=undef
+ checkbox_bromine=undef
+ checkbox_chlorine=undef
+ DATADIR=/home/masstrix3/data
+ BASE=/home/masstrix3/public_html/users/11121314465421347
+ ID=11121314465421347
+ EXEC=/home/masstrix3/exec
+ echo 'undef 0.5 red blue no undef undef undef undef'
undef 0.5 red blue no undef undef undef undef
+ echo '/home/masstrix3/data /home/masstrix3/public_html/users/11121314465421347 11121314465421347 /...
/home/masstrix3/data /home/masstrix3/public_html/users/11121314465421347 11121314465421347 /home/mas...
+ echo 'Running METABOLOMICS'
+ date
Tue Dec 13 14:47:02 CET 2011
+ echo ID=11121314465421347
++ hostname
+ '[' ibis12 = molerat ']'
++ hostname
+ '[' ibis12 = molerat ']'
+ echo /usr/bin:/bin
+ echo /home/masstrix3/data
+ grep = /home/masstrix3/public_html/users/11121314465421347/options
+ sed 's/=[\t ]*/='\''/'
+ sed 's/[\t ]*$/'\''/'
+ sed 's/ [ \t]*//'
+ sed 's/^/export /'
+ source /home/masstrix3/public_html/users/11121314465421347/options.sh
++ export ID=11121314465421347
++ ID=11121314465421347
++ export 'JOBID=human highlight genes'
++ JOBID='human highlight genes'
++ export EMAIL=ADMIN
++ export USERID=ADMIN
++ export PRIVAT=0
++ export MODE=pos
++ MODE=pos
++ export natrium=undef
++ natrium=undef
++ export potassium=undef
++ potassium=undef
++ export chlorine=undef
++ chlorine=undef
++ export bromine=undef
++ bromine=undef
++ export PPM=1.0
++ PPM=1.0
++ export ABS_M_Z=undef
++ ABS_M_Z=undef
++ export ORG=hsa
++ ORG=hsa
++ export DB=KEGGlipidiso
++ DB=KEGGlipidiso
+ rm /home/masstrix3/public_html/users/11121314465421347/options.sh
+ rm /home/masstrix3/public_html/users/11121314465421347/MASS.tsv
+ '[' KEGGlipidiso = KEGGlipidiso ']'
+ ln -sf /home/masstrix3/data/CORRECTED.MASS.KEGGLIPIDS.ISO.tsv /home/masstrix3/public_html/users/11...
+ '[' KEGGlipidiso = KEGGlipidnoiso ']'
+ '[' KEGGlipidiso = KEGGexpanded ']'
+ '[' KEGGlipidiso = MetaCyc ']'
+ '[' KEGGlipidiso = Lipids ']'
+ '[' '!' -e /home/masstrix3/public_html/users/11121314465421347/MASS.tsv ']'
+ echo ''
+ /home/masstrix3/exec/check_input_file.pl /home/masstrix3/public_html/users/11121314465421347
Use of uninitialized value $type_anno in string eq at /home/masstrix3/exec/check_input_file.pl line ...
Use of uninitialized value $type_anno in string eq at /home/masstrix3/exec/check_input_file.pl line ...
++ cat /home/masstrix3/public_html/users/11121314465421347/input.type
+ inputtype=mass
+ '[' mass == mass ']'
+ cat /home/masstrix3/public_html/users/11121314465421347/input
+ sed 's/^M//g'
+ grep '[0-9]'
+ sed '
s/  */\t/
+ mv /home/masstrix3/public_html/users/11121314465421347/input.tmp /home/masstrix3/public_html/users...
+ cat /home/masstrix3/public_html/users/11121314465421347/pathways.limit
+ sed 's/^M//g'
+ sed 's/[ \t]//g'
+ grep -v '^$'
+ mv /home/masstrix3/public_html/users/11121314465421347/pathways.limit.tmp /home/masstrix3/public_h...
+ cat /home/masstrix3/public_html/users/11121314465421347/genes.highlight
+ sed 's/^M//g'
+ sed 's/[ \t]//g'
+ grep -v '^$'
+ mv /home/masstrix3/public_html/users/11121314465421347/genes.highlight.tmp /home/masstrix3/public_...
+ '[' mass == mass ']'
+ echo 'mass input'
mass input
+ /home/masstrix3/exec/match_masses.pl /home/masstrix3/public_html/users/11121314465421347 /home/mas...
+ /home/masstrix3/exec/filter_isotopes.pl
Name "main::uniqueID" used only once: possible typo at /home/masstrix3/exec/filter_isotopes.pl line ...
15516 lines were read from file /home/masstrix3/public_html/users/11121314465421347/input
174294 lines were read from file /home/masstrix3/public_html/users/11121314465421347/MASS.tsv
searching for all corrected mass the closest reference mass
input masses scaled by 1, then shifted by 0; corrected by proton mass 
allowed max difference in mass: maxppm = 1.0
16509 lines read, 1393 kept (non-NA)
1098 lines were dropped
+ /home/masstrix3/exec/reformat_annotated_masses.pl /home/masstrix3/public_html/users/11121314465421...
+ /home/masstrix3/exec/create_affy_csv_files_and_foldchange.pl /home/masstrix3/data 1112131446542134...
+ /home/masstrix3/exec/test_KEGG_API.pl list hsa
+ cp /home/masstrix3/public_html/users/11121314465421347/orgpathwaylist /home/masstrix3/public_html/...
+ cat /home/masstrix3/public_html/users/11121314465421347/orgpathwaylist.full
retrieving all PATHWAYS for hsa from KEGG
path:hsa00010	Glycolysis / Gluconeogenesis - Homo sapiens (human)
path:hsa00020	Citrate cycle (TCA cycle) - Homo sapiens (human)
path:hsa00030	Pentose phosphate pathway - Homo sapiens (human)
path:hsa00040	Pentose and glucuronate interconversions - Homo sapiens (human)
path:hsa00051	Fructose and mannose metabolism - Homo sapiens (human)
path:hsa00052	Galactose metabolism - Homo sapiens (human)
path:hsa00053	Ascorbate and aldarate metabolism - Homo sapiens (human)
path:hsa00061	Fatty acid biosynthesis - Homo sapiens (human)
path:hsa00062	Fatty acid elongation - Homo sapiens (human)
path:hsa00071	Fatty acid metabolism - Homo sapiens (human)
path:hsa00072	Synthesis and degradation of ketone bodies - Homo sapiens (human)
path:hsa00100	Steroid biosynthesis - Homo sapiens (human)
path:hsa00120	Primary bile acid biosynthesis - Homo sapiens (human)
path:hsa00130	Ubiquinone and other terpenoid-quinone biosynthesis - Homo sapiens (human)
path:hsa00140	Steroid hormone biosynthesis - Homo sapiens (human)
path:hsa00190	Oxidative phosphorylation - Homo sapiens (human)
path:hsa00230	Purine metabolism - Homo sapiens (human)
path:hsa00232	Caffeine metabolism - Homo sapiens (human)
path:hsa00240	Pyrimidine metabolism - Homo sapiens (human)
path:hsa00250	Alanine, aspartate and glutamate metabolism - Homo sapiens (human)
path:hsa00260	Glycine, serine and threonine metabolism - Homo sapiens (human)
path:hsa00270	Cysteine and methionine metabolism - Homo sapiens (human)
path:hsa00280	Valine, leucine and isoleucine degradation - Homo sapiens (human)
path:hsa00290	Valine, leucine and isoleucine biosynthesis - Homo sapiens (human)
path:hsa00300	Lysine biosynthesis - Homo sapiens (human)
path:hsa00310	Lysine degradation - Homo sapiens (human)
path:hsa00330	Arginine and proline metabolism - Homo sapiens (human)
path:hsa00340	Histidine metabolism - Homo sapiens (human)
path:hsa00350	Tyrosine metabolism - Homo sapiens (human)
path:hsa00360	Phenylalanine metabolism - Homo sapiens (human)
path:hsa00380	Tryptophan metabolism - Homo sapiens (human)
path:hsa00400	Phenylalanine, tyrosine and tryptophan biosynthesis - Homo sapiens (human)
path:hsa00410	beta-Alanine metabolism - Homo sapiens (human)
path:hsa00430	Taurine and hypotaurine metabolism - Homo sapiens (human)
path:hsa00450	Selenocompound metabolism - Homo sapiens (human)
path:hsa00460	Cyanoamino acid metabolism - Homo sapiens (human)
path:hsa00471	D-Glutamine and D-glutamate metabolism - Homo sapiens (human)
path:hsa00472	D-Arginine and D-ornithine metabolism - Homo sapiens (human)
path:hsa00480	Glutathione metabolism - Homo sapiens (human)
path:hsa00500	Starch and sucrose metabolism - Homo sapiens (human)
path:hsa00510	N-Glycan biosynthesis - Homo sapiens (human)
path:hsa00511	Other glycan degradation - Homo sapiens (human)
path:hsa00512	Mucin type O-Glycan biosynthesis - Homo sapiens (human)
path:hsa00514	Other types of O-glycan biosynthesis - Homo sapiens (human)
path:hsa00520	Amino sugar and nucleotide sugar metabolism - Homo sapiens (human)
path:hsa00524	Butirosin and neomycin biosynthesis - Homo sapiens (human)
path:hsa00531	Glycosaminoglycan degradation - Homo sapiens (human)
path:hsa00532	Glycosaminoglycan biosynthesis - chondroitin sulfate - Homo sapiens (human)
path:hsa00533	Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human)
path:hsa00534	Glycosaminoglycan biosynthesis - heparan sulfate - Homo sapiens (human)
path:hsa00561	Glycerolipid metabolism - Homo sapiens (human)
path:hsa00562	Inositol phosphate metabolism - Homo sapiens (human)
path:hsa00563	Glycosylphosphatidylinositol(GPI)-anchor biosynthesis - Homo sapiens (human)
path:hsa00564	Glycerophospholipid metabolism - Homo sapiens (human)
path:hsa00565	Ether lipid metabolism - Homo sapiens (human)
path:hsa00590	Arachidonic acid metabolism - Homo sapiens (human)
path:hsa00591	Linoleic acid metabolism - Homo sapiens (human)
path:hsa00592	alpha-Linolenic acid metabolism - Homo sapiens (human)
path:hsa00600	Sphingolipid metabolism - Homo sapiens (human)
path:hsa00601	Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human)
path:hsa00603	Glycosphingolipid biosynthesis - globo series - Homo sapiens (human)
path:hsa00604	Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human)
path:hsa00620	Pyruvate metabolism - Homo sapiens (human)
path:hsa00630	Glyoxylate and dicarboxylate metabolism - Homo sapiens (human)
path:hsa00640	Propanoate metabolism - Homo sapiens (human)
path:hsa00650	Butanoate metabolism - Homo sapiens (human)
path:hsa00670	One carbon pool by folate - Homo sapiens (human)
path:hsa00730	Thiamine metabolism - Homo sapiens (human)
path:hsa00740	Riboflavin metabolism - Homo sapiens (human)
path:hsa00750	Vitamin B6 metabolism - Homo sapiens (human)
path:hsa00760	Nicotinate and nicotinamide metabolism - Homo sapiens (human)
path:hsa00770	Pantothenate and CoA biosynthesis - Homo sapiens (human)
path:hsa00780	Biotin metabolism - Homo sapiens (human)
path:hsa00785	Lipoic acid metabolism - Homo sapiens (human)
path:hsa00790	Folate biosynthesis - Homo sapiens (human)
path:hsa00830	Retinol metabolism - Homo sapiens (human)
path:hsa00860	Porphyrin and chlorophyll metabolism - Homo sapiens (human)
path:hsa00900	Terpenoid backbone biosynthesis - Homo sapiens (human)
path:hsa00910	Nitrogen metabolism - Homo sapiens (human)
path:hsa00920	Sulfur metabolism - Homo sapiens (human)
path:hsa00970	Aminoacyl-tRNA biosynthesis - Homo sapiens (human)
path:hsa00980	Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human)
path:hsa00982	Drug metabolism - cytochrome P450 - Homo sapiens (human)
path:hsa00983	Drug metabolism - other enzymes - Homo sapiens (human)
path:hsa01040	Biosynthesis of unsaturated fatty acids - Homo sapiens (human)
path:hsa01100	Metabolic pathways - Homo sapiens (human)
path:hsa02010	ABC transporters - Homo sapiens (human)
path:hsa03008	Ribosome biogenesis in eukaryotes - Homo sapiens (human)
path:hsa03010	Ribosome - Homo sapiens (human)
path:hsa03013	RNA transport - Homo sapiens (human)
path:hsa03015	mRNA surveillance pathway - Homo sapiens (human)
path:hsa03018	RNA degradation - Homo sapiens (human)
path:hsa03020	RNA polymerase - Homo sapiens (human)
path:hsa03022	Basal transcription factors - Homo sapiens (human)
path:hsa03030	DNA replication - Homo sapiens (human)
path:hsa03040	Spliceosome - Homo sapiens (human)
path:hsa03050	Proteasome - Homo sapiens (human)
path:hsa03060	Protein export - Homo sapiens (human)
path:hsa03320	PPAR signaling pathway - Homo sapiens (human)
path:hsa03410	Base excision repair - Homo sapiens (human)
path:hsa03420	Nucleotide excision repair - Homo sapiens (human)
path:hsa03430	Mismatch repair - Homo sapiens (human)
path:hsa03440	Homologous recombination - Homo sapiens (human)
path:hsa03450	Non-homologous end-joining - Homo sapiens (human)
path:hsa03460	Fanconi anemia pathway - Homo sapiens (human)
path:hsa04010	MAPK signaling pathway - Homo sapiens (human)
path:hsa04012	ErbB signaling pathway - Homo sapiens (human)
path:hsa04020	Calcium signaling pathway - Homo sapiens (human)
path:hsa04060	Cytokine-cytokine receptor interaction - Homo sapiens (human)
path:hsa04062	Chemokine signaling pathway - Homo sapiens (human)
path:hsa04070	Phosphatidylinositol signaling system - Homo sapiens (human)
path:hsa04080	Neuroactive ligand-receptor interaction - Homo sapiens (human)
path:hsa04110	Cell cycle - Homo sapiens (human)
path:hsa04114	Oocyte meiosis - Homo sapiens (human)
path:hsa04115	p53 signaling pathway - Homo sapiens (human)
path:hsa04120	Ubiquitin mediated proteolysis - Homo sapiens (human)
path:hsa04122	Sulfur relay system - Homo sapiens (human)
path:hsa04130	SNARE interactions in vesicular transport - Homo sapiens (human)
path:hsa04140	Regulation of autophagy - Homo sapiens (human)
path:hsa04141	Protein processing in endoplasmic reticulum - Homo sapiens (human)
path:hsa04142	Lysosome - Homo sapiens (human)
path:hsa04144	Endocytosis - Homo sapiens (human)
path:hsa04145	Phagosome - Homo sapiens (human)
path:hsa04146	Peroxisome - Homo sapiens (human)
path:hsa04150	mTOR signaling pathway - Homo sapiens (human)
path:hsa04210	Apoptosis - Homo sapiens (human)
path:hsa04260	Cardiac muscle contraction - Homo sapiens (human)
path:hsa04270	Vascular smooth muscle contraction - Homo sapiens (human)
path:hsa04310	Wnt signaling pathway - Homo sapiens (human)
path:hsa04320	Dorso-ventral axis formation - Homo sapiens (human)
path:hsa04330	Notch signaling pathway - Homo sapiens (human)
path:hsa04340	Hedgehog signaling pathway - Homo sapiens (human)
path:hsa04350	TGF-beta signaling pathway - Homo sapiens (human)
path:hsa04360	Axon guidance - Homo sapiens (human)
path:hsa04370	VEGF signaling pathway - Homo sapiens (human)
path:hsa04380	Osteoclast differentiation - Homo sapiens (human)
path:hsa04510	Focal adhesion - Homo sapiens (human)
path:hsa04512	ECM-receptor interaction - Homo sapiens (human)
path:hsa04514	Cell adhesion molecules (CAMs) - Homo sapiens (human)
path:hsa04520	Adherens junction - Homo sapiens (human)
path:hsa04530	Tight junction - Homo sapiens (human)
path:hsa04540	Gap junction - Homo sapiens (human)
path:hsa04610	Complement and coagulation cascades - Homo sapiens (human)
path:hsa04612	Antigen processing and presentation - Homo sapiens (human)
path:hsa04614	Renin-angiotensin system - Homo sapiens (human)
path:hsa04620	Toll-like receptor signaling pathway - Homo sapiens (human)
path:hsa04621	NOD-like receptor signaling pathway - Homo sapiens (human)
path:hsa04622	RIG-I-like receptor signaling pathway - Homo sapiens (human)
path:hsa04623	Cytosolic DNA-sensing pathway - Homo sapiens (human)
path:hsa04630	Jak-STAT signaling pathway - Homo sapiens (human)
path:hsa04640	Hematopoietic cell lineage - Homo sapiens (human)
path:hsa04650	Natural killer cell mediated cytotoxicity - Homo sapiens (human)
path:hsa04660	T cell receptor signaling pathway - Homo sapiens (human)
path:hsa04662	B cell receptor signaling pathway - Homo sapiens (human)
path:hsa04664	Fc epsilon RI signaling pathway - Homo sapiens (human)
path:hsa04666	Fc gamma R-mediated phagocytosis - Homo sapiens (human)
path:hsa04670	Leukocyte transendothelial migration - Homo sapiens (human)
path:hsa04672	Intestinal immune network for IgA production - Homo sapiens (human)
path:hsa04710	Circadian rhythm - mammal - Homo sapiens (human)
path:hsa04720	Long-term potentiation - Homo sapiens (human)
path:hsa04721	Synaptic vesicle cycle - Homo sapiens (human)
path:hsa04722	Neurotrophin signaling pathway - Homo sapiens (human)
path:hsa04724	Glutamatergic synapse - Homo sapiens (human)
path:hsa04725	Cholinergic synapse - Homo sapiens (human)
path:hsa04726	Serotonergic synapse - Homo sapiens (human)
path:hsa04727	GABAergic synapse - Homo sapiens (human)
path:hsa04728	Dopaminergic synapse - Homo sapiens (human)
path:hsa04730	Long-term depression - Homo sapiens (human)
path:hsa04740	Olfactory transduction - Homo sapiens (human)
path:hsa04742	Taste transduction - Homo sapiens (human)
path:hsa04744	Phototransduction - Homo sapiens (human)
path:hsa04810	Regulation of actin cytoskeleton - Homo sapiens (human)
path:hsa04910	Insulin signaling pathway - Homo sapiens (human)
path:hsa04912	GnRH signaling pathway - Homo sapiens (human)
path:hsa04914	Progesterone-mediated oocyte maturation - Homo sapiens (human)
path:hsa04916	Melanogenesis - Homo sapiens (human)
path:hsa04920	Adipocytokine signaling pathway - Homo sapiens (human)
path:hsa04930	Type II diabetes mellitus - Homo sapiens (human)
path:hsa04940	Type I diabetes mellitus - Homo sapiens (human)
path:hsa04950	Maturity onset diabetes of the young - Homo sapiens (human)
path:hsa04960	Aldosterone-regulated sodium reabsorption - Homo sapiens (human)
path:hsa04961	Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human)
path:hsa04962	Vasopressin-regulated water reabsorption - Homo sapiens (human)
path:hsa04964	Proximal tubule bicarbonate reclamation - Homo sapiens (human)
path:hsa04966	Collecting duct acid secretion - Homo sapiens (human)
path:hsa04970	Salivary secretion - Homo sapiens (human)
path:hsa04971	Gastric acid secretion - Homo sapiens (human)
path:hsa04972	Pancreatic secretion - Homo sapiens (human)
path:hsa04973	Carbohydrate digestion and absorption - Homo sapiens (human)
path:hsa04974	Protein digestion and absorption - Homo sapiens (human)
path:hsa04975	Fat digestion and absorption - Homo sapiens (human)
path:hsa04976	Bile secretion - Homo sapiens (human)
path:hsa04977	Vitamin digestion and absorption - Homo sapiens (human)
path:hsa04978	Mineral absorption - Homo sapiens (human)
path:hsa05010	Alzheimer's disease - Homo sapiens (human)
path:hsa05012	Parkinson's disease - Homo sapiens (human)
path:hsa05014	Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human)
path:hsa05016	Huntington's disease - Homo sapiens (human)
path:hsa05020	Prion diseases - Homo sapiens (human)
path:hsa05100	Bacterial invasion of epithelial cells - Homo sapiens (human)
path:hsa05110	Vibrio cholerae infection - Homo sapiens (human)
path:hsa05120	Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human)
path:hsa05130	Pathogenic Escherichia coli infection - Homo sapiens (human)
path:hsa05131	Shigellosis - Homo sapiens (human)
path:hsa05132	Salmonella infection - Homo sapiens (human)
path:hsa05133	Pertussis - Homo sapiens (human)
path:hsa05134	Legionellosis - Homo sapiens (human)
path:hsa05140	Leishmaniasis - Homo sapiens (human)
path:hsa05142	Chagas disease (American trypanosomiasis) - Homo sapiens (human)
path:hsa05143	African trypanosomiasis - Homo sapiens (human)
path:hsa05144	Malaria - Homo sapiens (human)
path:hsa05145	Toxoplasmosis - Homo sapiens (human)
path:hsa05146	Amoebiasis - Homo sapiens (human)
path:hsa05150	Staphylococcus aureus infection - Homo sapiens (human)
path:hsa05152	Tuberculosis - Homo sapiens (human)
path:hsa05160	Hepatitis C - Homo sapiens (human)
path:hsa05162	Measles - Homo sapiens (human)
path:hsa05164	Influenza A - Homo sapiens (human)
path:hsa05166	HTLV-I infection - Homo sapiens (human)
path:hsa05168	Herpes simplex infection - Homo sapiens (human)
path:hsa05200	Pathways in cancer - Homo sapiens (human)
path:hsa05202	Transcriptional misregulation in cancers - Homo sapiens (human)
path:hsa05210	Colorectal cancer - Homo sapiens (human)
path:hsa05211	Renal cell carcinoma - Homo sapiens (human)
path:hsa05212	Pancreatic cancer - Homo sapiens (human)
path:hsa05213	Endometrial cancer - Homo sapiens (human)
path:hsa05214	Glioma - Homo sapiens (human)
path:hsa05215	Prostate cancer - Homo sapiens (human)
path:hsa05216	Thyroid cancer - Homo sapiens (human)
path:hsa05217	Basal cell carcinoma - Homo sapiens (human)
path:hsa05218	Melanoma - Homo sapiens (human)
path:hsa05219	Bladder cancer - Homo sapiens (human)
path:hsa05220	Chronic myeloid leukemia - Homo sapiens (human)
path:hsa05221	Acute myeloid leukemia - Homo sapiens (human)
path:hsa05222	Small cell lung cancer - Homo sapiens (human)
path:hsa05223	Non-small cell lung cancer - Homo sapiens (human)
path:hsa05310	Asthma - Homo sapiens (human)
path:hsa05320	Autoimmune thyroid disease - Homo sapiens (human)
path:hsa05322	Systemic lupus erythematosus - Homo sapiens (human)
path:hsa05323	Rheumatoid arthritis - Homo sapiens (human)
path:hsa05330	Allograft rejection - Homo sapiens (human)
path:hsa05332	Graft-versus-host disease - Homo sapiens (human)
path:hsa05340	Primary immunodeficiency - Homo sapiens (human)
path:hsa05410	Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human)
path:hsa05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human)
path:hsa05414	Dilated cardiomyopathy - Homo sapiens (human)
path:hsa05416	Viral myocarditis - Homo sapiens (human)
+ cat /home/masstrix3/public_html/users/11121314465421347/pathways.limit
++ cat /home/masstrix3/public_html/users/11121314465421347/pathways.limit
++ wc -c
+ NPW=0
+ '[' 0 -ge 2 ']'
++ cat /home/masstrix3/public_html/users/11121314465421347/pathwaylist
++ wc -l
cat: /home/masstrix3/public_html/users/11121314465421347/pathwaylist: No such file or directory
+ NPW=0
+ '[' 0 -lt 1 ']'
+ echo -e 'path:hsa00010\tGlycolysis / Gluconeogenesis '
+ echo path:hsa00010
+ cat /home/masstrix3/public_html/users/11121314465421347/pathwaylist
+ awk '{print $1}'
+ read pw
+ /home/masstrix3/exec/test_KEGG_API.pl /home/masstrix3/public_html/users/11121314465421347/masses.a...
--2011-12-13 14:51:10--  http://soap.genome.jp/tmp/mark_pathway_www_api.132378538911930/map00010.png...
Resolving soap.genome.jp...
Connecting to soap.genome.jp||:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 26853 (26K) [image/png]
Saving to: `/home/masstrix3/public_html/users/11121314465421347/map00010.png'

     0K .......... .......... ......                          100% 42.7K=0.6s

2011-12-13 14:51:11 (42.7 KB/s) - `/home/masstrix3/public_html/users/11121314465421347/map00010.png'...

--2011-12-13 14:51:11--  http://www.genome.ad.jp/dbget-bin/show_pathway?map00010
Resolving www.genome.ad.jp...
Connecting to www.genome.ad.jp||:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://www.genome.jp/dbget-bin/show_pathway?map00010 [following]
--2011-12-13 14:51:12--  http://www.genome.jp/dbget-bin/show_pathway?map00010
Resolving www.genome.jp...
Reusing existing connection to www.genome.ad.jp:80.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/html]
Saving to: `STDOUT'

     0K .......... .......... .......... .......... .......... 84.4K
    50K .......... .......... .......... .......... ..........  169K
   100K .......... ....                                        50.0K=1.2s

2011-12-13 14:51:13 (97.2 KB/s) - `-' saved [117287]

+ cat /home/masstrix3/public_html/users/11121314465421347/path:hsa00010.KEGGout
affychip: undef organism:hsa
$mypw path:hsa00010 $stdpw path:map00010
reading list of genes to be highlighted
3 genes in highlight list
no genes in expression annotation list
search KEGG for
INFO-Gorg-1: ko:K01835
search KEGG for hk2:
INFO-Gorg-1: ko:K00844
INFO-Gorg-1: ko:K01835
search KEGG for K01810:
INFO-Gorg-1: ko:K01810
read stdpw compounds from file
INFO-Cmap: cpd:C00118
INFO-Cmap: cpd:C06188
INFO-Cmap: cpd:C01172
INFO-Cmap: cpd:C16255
INFO-Cmap: cpd:C00668
INFO-Cmap: cpd:C00024
INFO-Cmap: cpd:C15973
INFO-Cmap: cpd:C00631
INFO-Cmap: cpd:C01451
INFO-Cmap: cpd:C01159
INFO-Cmap: cpd:C00267
INFO-Cmap: cpd:C00036
INFO-Cmap: cpd:C00074
INFO-Cmap: cpd:C06186
INFO-Cmap: cpd:C00103
INFO-Cmap: cpd:C00197
INFO-Cmap: cpd:C05125
INFO-Cmap: cpd:C00033
INFO-Cmap: cpd:C15972
INFO-Cmap: cpd:C05345
INFO-Cmap: cpd:C00111
INFO-Cmap: cpd:C00236
INFO-Cmap: cpd:C00186
INFO-Cmap: cpd:C00221
INFO-Cmap: cpd:C05378
INFO-Cmap: cpd:C00068
INFO-Cmap: cpd:C00022
INFO-Cmap: cpd:C00469
INFO-Cmap: cpd:C00084
INFO-Cmap: cpd:C00031
INFO-Cmap: cpd:C06187
read compound from FILE
INFO-Corg: cpd:C15973
INFO-Corg: cpd:C00236
INFO-Corg: cpd:C00221
INFO-Corg: cpd:C00186
INFO-Corg: cpd:C16255
INFO-Corg: cpd:C00024
INFO-Corg: cpd:C00631
INFO-Corg: cpd:C01159
INFO-Corg: cpd:C00033
INFO-Corg: cpd:C00022
INFO-Corg: cpd:C00068
INFO-Corg: cpd:C00469
INFO-Corg: cpd:C01172
INFO-Corg: cpd:C00668
INFO-Corg: cpd:C00267
INFO-Corg: cpd:C00036
INFO-Corg: cpd:C00074
INFO-Corg: cpd:C00197
INFO-Corg: cpd:C00031
INFO-Corg: cpd:C00084
INFO-Corg: cpd:C00118
INFO-Corg: cpd:C00103
INFO-Corg: cpd:C15972
INFO-Corg: cpd:C05345
INFO-Corg: cpd:C00111
INFO-Corg: cpd:C05378
291 annotated peaks were read from file /home/masstrix3/public_html/users/11121314465421347/masses.a...
INFO-Corgid: cpd:C00074
Grenzen:-0.5 0.5
RESULT: path:hsa00010 perl /home/masstrix3/exec/specificity.pl 31 26 1 1 0.838709677419355
coloring using KEGG API color_pathway_by_objects method
wget http://soap.genome.jp/tmp/mark_pathway_www_api.132378538911930/map00010.png --directory-prefix=...
+ read pw
+ ls /home/masstrix3/public_html/users/11121314465421347/map00010.png
+ grep -h RESULT /home/masstrix3/public_html/users/11121314465421347/path:hsa00010.KEGGout
+ echo 'Finishing METABOLOMICS'
+ date

KEGG Data is provided by the Kanehisa Laboratories for academic use. Any commercial use of KEGG data requires a license agreement from Pathway Solutions Inc. The Helmholtz Zentrum München imprint applies. If you find results from this site helpful for your research, please cite:

K. Suhre and P. Schmitt-Kopplin, MassTRIX: Mass TRanslator Into Pathways, Nucleic Acids Research, Volume 36, Web Server issue, W481-W484, 2008.

This page is maintained by Brigitte Waegele and Karsten Suhre, last modification: 07 December 2011

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